Bruce Randall Donald -- Publications
Professor of Computer Science, Biochemistry, and Chemistry
Duke University

Quick Links:
Books - Papers - Cover Articles - Machine Learning/AI - Protein Structures - By topic - Categories/Indexes - Movies - Lab YouTube Channel - OspreyTube - Papers Before 1994 - Dissertations
My C.V. (PDF) contains the most compact publications list.

Books

• Algorithms in Structural Molecular Biology.
  MIT Press (2011).
  464 pages + 52 color plates.
  
  See the Book Web Page
  Preview
  Table of Contents (PDF)
  Sample Chapter (PDF)
  
  
  
• Symbolic and Numerical Computation for Artificial Intelligence,
  Academic Press, Harcourt Jovanovich, (London: 1992) (with D. Kapur and J. Mundy). 369 pp. ISBN 0122205359.
  • This book is available on Amazon.com and other book sellers.
  • PDF versions of the chapters are here.
  
  
• New Directions in Algorithmic and Computational Robotics (with K. Lynch and D. Rus). A. K. Peters, Ltd. (Boston: 2001), 408 pp. ISBN: 1-56881-125-X
  • Available on Amazon

• See all 5 books

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Cover Articles



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Finding Papers

• Many of my papers are provided below.
• MyBibliography (NCBI/NLM) contains Medline-indexed journal articles, plus a subset of my articles and books in engineering, robotics, and nanoscience.
• Protein structures determined in our papers.
• The complete set of my papers and books, together with free PDFs, is easily found using Google Scholar.

Selected Recent Papers

• Papers by Topic
  • Machine Learning/AI
  • Systems Biology
  • Structural Molecular Biology and Biochemistry
    • Protein Structure Gallery
      • Search PDB (NCBI/NLM) for all our protein structures (NMR, X-ray)
  • Computational Molecular Biology
  • Neuroscience and Nanotechnology
  • MicroElectroMechanical Systems (MEMS), Nanoscience, and Microrobotics
  • Robotics
  • Mobile Robotics
  • Motion Planning and Geometric Algorithms
    • Kinodynamic Planning
  • Computer Graphics
  • Computational Geometry
• Cover Articles
• Movies: [Robots, Microrobots and MEMS, MEMS ciliary arrays and distributed manipulation]

  Protein Design by Provable Algorithms (in Comm. ACM, 2019).

  • We have a Youtube channel on Osprey.
  • Our lab has a YouTube channel:
    http://www.youtube.com/user/labdonald/videos, (www.youtube.com/@Donaldlab)
    with many videos describing our research.
    • OspreyTube
    Most of these videos are on microrobotics and nanoscience. While a lot of our work now is on structural and computational biology, we have not made many videos on those topics yet. However, we have written a textbook and plenty of papers you can read on structural and computational biology and biochemistry.
    However, OspreyTube is growing.
    Please note that not all of our videos above are on YouTube because some, for example, are hosted in a lecture series at MIT.
    Some of our videos are copyrighted by the music publisher (because of the music) and therefore are here, here, or here, or here. Or Here (Siggraph 1990).
• Indexes* and Reviews of Our Papers
  *Indicates indexes and reviews of our papers not written/compiled by our group.
  *Please note: Most indexes and collections of our papers are incomplete since the computer science indexes do not list the biomedical journals, and Medline does not list the computer science and robotics papers. Only Google Scholar seems reasonably complete.
  • *Comment in The Lancet (2019) on the clinical trials of the designed antibody VRC07-523LS in our Jour. Virology paper.
    
  • *Computer Scientist in Profile: Bruce R. Donald (by Amarda Shehu). ACM SIGBioinformatics Record 2014; 4(1) 5-7. doi.org/10.1145/2584125.2584126.
  • *Computational protein design to circumvent antibiotic resistance, The Molecular Model (2020).
  • *Data analysis (by S. Aerni and E. Eskin) of the impact of our lab on RECOMB.
  • *Review of our papers on protein design (by SM Lippow & B Tidor). Progress in computational protein design. Curr Opin Biotechnol. 2007; Medline, PMID 17644370.
  • Indexes* of papers listed on
    • *MyBibliography (NCBI/NLM)
    • *Medline
    • *Google Scholar
    • *DBLP Bibliography Server
    • Special Issue of Algorithmica (2000)
    • My C.V. (PDF) (contains a complete list of publications)
    • Current Research; Donald Lab
    • Publications prior to 1994; Publications not listed here

Predicting Cancer Resistance Mutations by Pareto Optimization Over Multistate Protein Design
Predicting Resistance Mutations using Protein Design Algorithms. PNAS (2010).
	Computational Structure-Based Redesign of Enzyme Activity. PNAS (2009).
Protein Design by Provable Algorithms (in Comm. ACM, 2019).
	Computational design of a tight binder to KRas, an “undruggable” cancer target PLoS Computational Biology 2020.
	Cover Article, Chemistry & Biology 2007. [Caption]
	Redesigning the PheA Domain of Gramicidin Synthetase. Biochemistry 2006; 45 (51):15495-15504.
	Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis. (J. Biol. Chem. 2003).
	Cover article, J. Eukaryotic Microbiology (2003).
	Cover article, PROTEINS (2012).
Complete ensemble of NMR structures of the unphosphorylated human cardiac phospholamban pentamer. PDB ID: 2HYN (Proteins, 2006)

List of Selected Papers, Broken into categories

• Machine Learning, Artificial Intelligence, & Applications of ML/AI to Science and Engineering

  • Predicting Affinity Through Homology (PATH): Interpretable Binding Affinity Prediction with Persistent Homology, bioarXiv, doi: https://doi.org/10.1101/2023.11.16.567384 (2024)
  • "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum," (with R. Lilien and H. Farid), Journal of Computational Biology, 10(6) 2003, pp. 925-946.
    • [Medline, PDF]
    • [The figures may look better in this pdfLaTeX reprint]
  • "HASH: a Program to Accurately Predict Protein Hα (H-alpha) Shifts from Neighboring Backbone Shifts" (with J. Zeng, and P. Zhou). Journal of Biomolecular NMR 2012; Dec 16.
    • [PDF]
  • Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
    • [Abstract, PDF]
  • Symbolic and Numerical Computation for Artificial Intelligence,
    Academic Press, Harcourt Jovanovich, (London: 1992) (with D. Kapur and J. Mundy). 369 pp. ISBN 0122205359.
  • Improved HIV-1 Neutralization Breadth and Potency of V2-Apex Antibodies by In Silico Design (with G. Holt, J. Gorman, S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder, M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose, and P. Kwong). Cell Reports (2023).
    • [PDF, html, PDF with SI/SR ]
  • LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency (with M. Hallen and J. Jou). Journal of Computational Biology 2016 Sep 28. PMID: 27681371
    The accepted manuscript has higher resolution figures than the published PDF:
    [ published journal PDF, SI, Accepted MS]

    This journal paper is a revised paper based on the earlier Conference version:

    LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency (with M. Hallen and J. Jou). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Los Angeles, CA, April, 2016. In Research in Computational Molecular Biology, Lecture Notes in Bioinformatics (LNBI), Springer-Verlag (Berlin), Volume 9649, 2016, pp. 122-136.

  • A compact representation of continuous energy surfaces for more efficient protein design (with M. Hallen and P. Gainza). Journal of Chemical Theory and Computation. 2015; 11(5):2292-2306.
    • [PDF, Abstract]

    Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with many videos describing our mobile robotics research.

  • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
    • [PDF]
  • Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches (with K. Hamaguchi, K. Tschida, I. Yoon, and R. Mooney). eLife 2014; 3:e01833. http://dx.doi.org/10.7554/eLife.01833
  • Distributed Manipulation of Multiple Objects Using Ropes, (with L. Gariepy and D. Rus), Proc. IEEE International Conference on Robotics and Automation (ICRA), San Francisco (April, 2000) pp. 450-457.
  • Practical Mobile Robot Self-Localization (with J. Howell) Proceedings, International Conference on Robotics and Automation, San Francisco, CA, April 24-28, 2000. pp. 3485-3492.

    Movie, 4:30, Quicktime w/Sorenson codec, max 250 kb/s (42MB)	mapmaking-movie-5.250kbit.mov
    Movie, 4:30, Quicktime w/Sorenson codec, max 100 kb/s (26MB)	mapmaking-movie-5.100kbit.mov
    The paper (Gzipped PostScript) (0.8 MB)	ICRA'2000 paper

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.
  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.
  • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000).
  • Experiments in Constrained Prehensile Manipulation: Distributed Manipulation with Ropes, with Larry Gariepy and Daniela Rus, In Experimental Robotics VI, Lecture Notes in Control and Information Sciences, Vol. 250, eds. P. Corke, Springer-Verlag, (2000).

  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Information Invariants for Distributed Manipulation (with J. Jennings and D. Rus) in International Journal of Robotics Research, Vol. 16, No. 5 (1997). pp. 673-702.
    • Here are the galleys from MIT Press (7/14/97).
    • Technical Report (1994) [TR FTP]
    • [Movie]

  • B. R. Donald, J. Jennings, and D. Rus, Minimalism + Distribution = Supermodularity [TR FTP], Journal of Experimental and Theoretical Artificial Intelligence (JETAI), Special issue on Software Architectures for Hardware Agents; Vol. 9 No. 2-3 (1997) pp. 293-321.
    • [PDF]

  • . On Information Invariants in Robotics. Artificial Intelligence 72 (Jan, 1995) pp. 217-304.
    • [ Abstract, PDF, Accepted Manuscript ]

  • Cost-effective, Capable, and Configurable Multiple Robots: A Report to the ARPA ISAT Study Group, Summer, 1996 (with J. Jennings and D. Rus).
  • R.G. Brown and J.S. Jennings. A pusher/steerer model for strongly cooperative mobile robot cooperation. In IEEE/RSJ IROS, pages 562-568, 1995.
  • Moving Furniture with Teams of Automonous Mobile Robots [TR FTP], (with J. Jennings and D. Rus) in

    Proc. IEEE/Robotics Society of Japan International Workshop on Intelligent Robots and Systems, (IROS) Pittsburgh, PA (1995).

  • .
    Program Mobile Robots in Scheme (with J. Rees) Proc. IEEE International Conference on Robotics and Automation Nice, France (May, 1992), pp. 2681-2688.
    
    [PDF]
    Many people do not realize that the title of this paper is in the hortatory subjunctive mode. It should be read as:
    Program Mobile Robots in Scheme! Note the exclamation point.

  • Information Invariants for Distributed Manipulation [TR FTP] (with J. Jennings and D. Rus) in The First Workshop on the Algorithmic Foundations of Robotics, A. K. Peters, Boston, MA. ed. R. Wilson and J.-C.Latombe (1994).
    • [Movie]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • Towards a Theory of Information Invariants for Cooperating Autonomous Mobile Robots, (with J. Jennings and D. Rus) International Symposium of Robotics Research (ISRR). Hidden Valley, PA (October 2, 1993).
  • Sensor Interpretation and Task-Directed Planning Using Perceptual Equivalence Classes (with J. Jennings). Proc. IEEE International Conference on Robotics and Automation, Sacramento, CA (April, 1991), pp. 190-197.
    • [PDF]

  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.

  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [PDF] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
    • [PDF]
    Other versions (Figures may look better in the TR):
    
    Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
    • [PDF]
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [PDF] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
    • [PDF]
    Other versions (Figures may look better in the TR):
    
    Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
    • [PDF]
  • Kinodynamic Motion Planning [PDF] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
    • [PDF]
    Other versions (Figures may look better in the TR):
    
    Kinodynamic Motion Planning - TR version [TR FTP] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
    • [PDF]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • ``The Motion of Planar Compliantly-Connected Rigid Bodies in Contact, with Applications to Automatic Fastening,'' B. R. Donald and D. Pai. International Journal of Robotics Research 12(4), August 1993, pp. 307-338.
    • [PDF]
  • ``Symbolic Methods for the Simulation of Planar Mechanical Systems in Design,'' B. R. Donald and D. Pai. in Symbolic and Numerical Computation for Artificial Intelligence, (ed. B. Donald et al.) Academic Press, Harcourt Jovanovich, (London: 1992), pp. 245-258.
  • Planning Multi-Step Error Detection and Recovery Strategies. International Journal of Robotics Research, 9(1), 1990. pp. 3-60.
    • [PDF]
  • Simplified Voronoi Diagrams (with J. Canny). Discrete and Computational Geometry 3:219-236 (1988).
    • [PDF]
  • A Geometric Approach to Error Detection and Recovery for Robot Motion Planning with Uncertainty, Artificial Intelligence, 1988: 37(1-3), pp. 223-271.
    • [PDF]
  • A Search Algorithm for Motion Planning with Six Degrees of Freedom, Artificial Intelligence 31(3), 1987. pp. 295-353.
    • [PDF]
  • Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots (with C. Levey, C. McGray, I. Paprotny, and D. Rus). International Journal of Robotics Research 2013; 32(2): 218-246.
    • [Abstract, PDF]
  • Turning-rate Selective Control: A New Method for Independent Control of Stress-engineered MEMS Microrobots (with C. Levey and I. Paprotny). Proceedings of Robotics: Science and Systems Conference (RSS), University of Sydney, Sydney, NSW, Australia. July 9-13, 2012 (In press).
    • [Abstract, PDF]
  • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
    • [PDF]
  • Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording (with I. Borzenets, I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of Applied Physics 2012; 111(7):74703-747036. doi: 10.1063/1.3702802.
    • [Summary, PDF]
  • Simultaneous Control of Multiple MEMS Microrobots (with C. Levey, I. Paprotny, and D. Rus). Proceedings of the Eighth International Workshop on the Algorithmic Foundations of Robotics (WAFR), Guanajuato, Mexico, December 7-9, 2008.
    Book chapter version (final) appears in: Springer Tracts on Advanced Robotics, 57, Springer-Verlag (Berlin), (2010), pp. 69-84.
    • [PDF, Supplementary Material]
  • Planar Microassembly by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Journal of Microelectromechanical Systems 2008; 17(4): 789-808.
    • [PDF, Video, Supporting Material, Ballet video, Youtube videos, Movies ]
  • Assembly of Planar Structures by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Hilton Head Workshop: A Solid-State Sensors, Actuators and Microsystems Workshop pp. 202-207. June 1-2, 2008, Hilton Head, SC.
    • [PDF, Video, Supporting Material, Ballet video, Youtube videos]
  • A Steerable, Untethered MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). In Robotics Research, Springer Tracks in Advanced Robotics 28, ed. S. Thrun, et al., Springer-Verlag (Berlin) 2007, pp. 337-356.
  • An Untethered, Electrostatic, Globally-Controllable MEMS Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). Journal of Microelectromechanical Systems, 2006; 15(1):1-15.
    • [PDF, Full text at IEEE, Supplementary Material (Videos)]
  • A Steerable, Untethered, 250 x 60 µm MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). 12th International Symposium of Robotics Research (ISRR), October 12-15, 2005, San Francisco, CA.
  • Power Delivery and Locomotion of Untethered Micro-Actuators (with C. Levey, C. McGray, D. Rus, and M. Sinclair). Journal of Microelectromechanical Systems 2003; 10(6):947-959.
    • [PDF, Movies]
  • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair). in Robotics Research eds. P. Dario and R. Chatila. Springer-Verlag (London) 2005, pp.502--516.
  • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair) 11^th International Symposium of Robotics Research (ISRR), October 19-22, 2003, Siena, Italy.
  • Power Delivery and Locomotion of Untethered Micro-Actuators, (with C. Levey, C. McGray, D. Rus, and M. Sinclair) IEEE MEMS (Proc. IEEE International Conference on Micro Electro Mechanical Systems), Kyoto, Japan, January 19-23, 2003. pp.124-129.
    • [PDF, Movies]
  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE Transactions on Robotics and Automation, 16(2), April 2000, pp. 157-170.
    • [Abstract, PDF]

  • Fully Programmable MEMS Ciliary Actuator Arrays for Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G.Kovacs), the IEEE International Conference on Robotics and Automation (ICRA) San Francisco (April, 2000) pp. 1101-1108.
  • Sensorless Manipulation Algorithms Using a Vibrating Surface, (with K.-F. Böhringer, V. Bhatt, and K. Goldberg) Algorithmica 26(3/4), March/April (2000) pp. 389-429.

  • CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) Journal of Microelectromechanical Systems, vol. 8, No. 4 (Dec. 1999), pp. 483-496.
    • [PDF] B&W version of published paper
  • "A Single Universal Force Field Can Uniquely Pose Any Part Up To Symmetry," (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki) 9th International Symposium of Robotics Research (ISRR) Snowbird, Utah October 9-12 (1999).
    • [PDF]
  • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000):
    1. CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs).
    2. A Distributed, Universal Device for Planar Parts Feeding: Unique Part Orientation in Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki).
    3. Constrained Prehensile Manipulation: Distributed Manipulation with Ropes (with L. Gariepy and D. Rus).
  • CMOS Integrated Organic Ciliary Actuator Array as a General-Purpose Micromanipulation Tool (with J. Suh, B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation, (Detroit) May 11, 1999.
  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation (Detroit) May 11, 1999.
  • Algorithmic MEMS, (with K.-F. Böhringer), Invited lecture at the Third International Workshop on the Algorithmic Foundations of Robotics (WAFR), Houston, TX (March, 1998). Book version: In Robotics: The Algorithmic Perspective, ed. P. Agarwal et al., A. K. Peters, Natick, MA (1998). pp. 1-20.
  • Computational Methods for the Design and Control of MEMS Micromanipulator Arrays (with K.-F. Böhringer, G. Kovacs, N. MacDonald, and J. Suh) IEEE Computational Science and Engineering, Vol. 4, No. 1. Special Issue on Computational MEMS (Jan-March 1997). pp. 17-29.
    • [PDF]
  • On The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Discrete and Computational Geometry, vol. 22 (1999), pp. 269-285.
  • Programmable Vector Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders, [TR FTP] (with K.-F. Böhringer, and N. C. MacDonald), (International Journal of Robotics Research). vol. 18(2), pp. 168-200 (1999).
    • Galleys from IJRR: [PDF]
  • Micro Contacts and Micro Manipulation with MEMS Actuator Arrays, (with K.-F. Böhringer IEEE International Conference on Robotics and Automation, Workshop on Modeling, Contact Analysis, and Simulation of Mechanical Systems in Robotics and Manufacturing, (Belgium, 1998).
  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • Vector Fields for Task-Level Distributed Manipulation: Experiments with Organic Micro Actuator Arrays [TR FTP], (with K.-F. Böhringer, J. Suh, and G. Kovacs) in Proc. IEEE International Conference on Robotics and Automation, Albuquerque, NM (1997). pp 1779-1786.
  • The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields [TR FTP], (with K.-F. Böhringer, and D. Halperin) 13th Proc. ACM Symposium on Computational Geometry, Nice, France (1997) pp. 457-459.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Single-Crystal Silicon Actuator Arrays for Micro Manipulation Tasks [TR FTP], IEEE Workshop on Micro Electro Mechanical Systems (MEMS), San Diego, California (February 1996).

• Systems Biology

  • Improved HIV-1 Neutralization Breadth and Potency of V2-Apex Antibodies by In Silico Design (with G. Holt, J. Gorman, S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder, M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose, and P. Kwong). Cell Reports (2023).
    • [PDF, html, PDF with SI/SR ]
  • Disruptor: Computational identification of oncogenic mutants disrupting protein interactions (with N. Guerin, V.Kugler, A. Lieb, E. Stefan, and T. Kaserer). Communications Biology (Nature Publishing Group) (2023)
    • [PDF, html]
  • Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from Chinavia ubica and Murgantia histrionica targeting E. coli LptA (with K. Huynh, A. Kibrom and P. Zhou). Journal of Structural Biology: X. (2023).
    • [PDF, html]
  • Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR (with N. Guerin and T. Kaserer). Cell STAR (Structured Transparent Accessible Reproducible) Protococols 2023; 4(2):102170. doi: 10.1016/j.xpro.2023.102170.
    • [PDF, html]
  • RESISTOR: An algorithm for predicting resistance mutations using Pareto optimization over multistate protein design and mutational signatures (with N. Guerin and T. Kaserer).
    Journal: Cell Systems 2022; (13)10: 830-843 [PDF, at journal], and
    Video from Conference: RECOMB (May, 2022), San Diego.
  • Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus (with S. Wang, S. Reeve, G. Holt A. Ojewole, M. Frenkel, P. Gainza, S. Keshpeddy, V. Fowler, and D. Wright). PLoS Computational Biology 2022; 18(2): e1009855. doi: https://doi.org/10.1371/journal.pcbi.1009855 . Cover Article.
  • Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches (with K. Hamaguchi, K. Tschida, I. Yoon, and R. Mooney). eLife 2014; 3:e01833. http://dx.doi.org/10.7554/eLife.01833
  • Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
    • [Abstract, PDF]
  • "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum," (with R. Lilien and H. Farid), Journal of Computational Biology, 10(6) 2003, pp. 925-946.
    • [Medline, PDF]
    • [The figures may look better in this pdfLaTeX reprint]
  • Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.
    • [Medline, PDF, Full text (at JBC), PDB Structure 1QZF]
  • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
    • The version on the Oxford (Bioinformatics) website is messed up, and this version is easier to read. (They did not correct a printer's error, and the SI has vanished). This version corrects both of the journal's errors.
      Below you can read the whole story:
      • [Medline, PDF, Erratum ]
      • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of Computational Biology, 8(1):19-36, 2001.
    • [Medline, PDF]
      
    • [The figures look better in this pdfLaTeX reprint]
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) Proc. the 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA (pp. 13-24).
    • [Medline]
  • "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns", (with C. Langmead, A. Yan, and C. R. McClung), Journal of Computational Biology 10(3-4) 2003, pp. 521-536.
    • [Medline, PDF]
    • [The figures may look better in this pdfLaTeX reprint]
  • "A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns," (with C. Langmead and C. R. McClung) Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 14-16, 2002) pp. 237-245.
    • [Medline, Abstract, PDF]
  • Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns, (with C. Langmead, T. Yan, and C. R. McClung), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). pp. 205-215.
    • [Abstract, PDF]
  
  

• Structural Molecular Biology, Biochemistry, & Computational Molecular Biology

• Structural Molecular Biology and Biochemistry

  • DexDesign: an osprey-based algorithm for designing de novo D-peptide inhibitors. (with N. Guerin, H. Childs and P. Zhou). Protein Engineering, Design, and Selection. 2024; 37:gzae007. doi: 10.1093/protein/gzae007. PMID: 38757573
    • [PDF]
  • Protocol for Designing De Novo Noncanonical Peptide Binders in Osprey (with N. Guerin, H. Childs, and P. Zhou) J Comput Biol. 2024 Oct 4. doi: 10.1089/cmb.2024.0669. PMID: 39364612
    • [PDF]
  • DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors (with N. Guerin, H. Childs, and P. Zhou). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Boston. (April 29-May 2, 2024).
    In Lecture Notes in Computer Science 14758, Springer (Cham, Schweizerische Eidgenossenschaft) pp. 336-249.
  • Improved HIV-1 Neutralization Breadth and Potency of V2-Apex Antibodies by In Silico Design (with G. Holt, J. Gorman, S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder, M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose, and P. Kwong). Cell Reports (2023).
    • [PDF, html, PDF with SI/SR ]
  • Disruptor: Computational identification of oncogenic mutants disrupting protein interactions (with N. Guerin, V.Kugler, A. Lieb, E. Stefan, and T. Kaserer). Communications Biology (Nature Publishing Group) (2023).
    • [PDF, html]
  • Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from Chinavia ubica and Murgantia histrionica targeting E. coli LptA (with K. Huynh, A. Kibrom and P. Zhou). Journal of Structural Biology: X. (2023).
    • [PDF, html]
  • Non-canonical inhibitors target the CAL binding site: new approaches to stabilize functional ΔF508-CFTR (with N. Gill, J. Amacher, P. Cushing, Y. Zhao, L. Wallace, A. Pletnev, M. Spaller, S. Cullati, S. Gerber, P. Boisguerin, D. Casalena, D. Auld, S. Wang, and D. Madden). 2023 European Cystic Fibrosis Society Conference. Dubrovnik, Croatia March 29-April 1 2023.
  • Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from Chinavia ubica and Murgantia histrionica targeting E. coli LptA (with K. Huynh, A. Kibrom and P. Zhou).
    • American Society for Biochemistry and Molecular Biology, Discover BMB Conference, Seattle, WA. March, 2023.
    • Journal of Biological Chemistry (2023) 299:(3):S640.
  • Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus (with S. Wang, S. Reeve, G. Holt A. Ojewole, M. Frenkel, P. Gainza, S. Keshpeddy, V. Fowler, and D. Wright). PLoS Computational Biology 2022; 18(2): e1009855. doi: https://doi.org/10.1371/journal.pcbi.1009855 . Cover Article.
  • Provable algorithms for ensemble-based computational protein design and the redesign of the KRas:RAF-kinase protein:protein interface (with A. Lowegard, M. Frenkel, J. Jou, A. Ojewole, and G. Holt). PLoS Computational Biology 2020; 16(6): e1007447. PMID: 32511232
    
    • [PDF, Supporting Information, Response to Reviewers, Peer Review History]
    • Preprint on BioRχiv
      
  • Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk). 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), vol. 129. pp. 2:1. Schloss Dagstuhl -- Leibniz-Zentrum für Informatik. doi: 10.4230/LIPIcs.SoCG.2019.2
    • [PDF]
  • Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand (with G. Holt, J. Jou, N. Gill, A. Lowegard, J. Martin, and D. Madden). Jour. Physical Chemistry B. 2019; 123(49):10441-10455. PMID: 31697075
    • [ PDF, Supporting Information]
      
  • Toward Broad Spectrum DHFR inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus. (with S. Reeve, D. Si, J. Krucinska, Y. Yan, K. Viswanathan, S. Wang, G. Holt, M. Frenkel, A. Ojewole, A. Estrada, S. Agabiti, J. Alverson, N. Gibson, N. Priestly, A. Wiemer, and D. Wright).
    ACS Infectious Diseases 2019; 5(11):1896-1906. .
    (doi: 10.1021/acsinfecdis.9b00222)
    Preprint on BioRχiv 648808; doi: https://doi.org/10.1101/648808
  • Protein Design by Provable Algorithms (with M. Hallen). Communications of the ACM, 2019; 61(10): 76-84. 10.1145/3338124.
    • [PDF, html, video]
  • Continuous interdomain orientation distributions reveal components of binding thermodynamics (with Y. Qi, J. Martin, A. Barb, F. Thelot, Anthony Yan, and T. Oas). Journal of Molecular Biology 2018; 430(18 Pt B): 3412-3426.
    • We have a YouTube playlist devoted to this topic.
  • OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features (with J. Martin, A. Lowegard, M. Frenkel, M.. Hallen, A. Ojewole, J. Jou, S. Wang, and G. Holt).
    Journal of Computational Chemistry 2018; 39(30): 2494-2507 Cover article.
    Available here:
    [Journal of Computational Chemistry].
    Cover Image (Osprey)
    [PDF of paper]
    [Accepted MS, Download Code]
    This work was presented at:
    Structural Bioinformatics and Computational Biophysics (3DSIG) track of ISMB. Chicago, Il. July 6-12, 2018. (Selected for Oral Presentation).
  • A critical analysis of computational protein design with sparse residue interaction graphs (with S. Jain, J. Jou, and I. Georgiev). PLoS Comput. Biol. 2017 Mar 30;13(3):e1005346. doi: 10.1371/journal.pcbi.1005346.
    • [PDF, HTML]
  • OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design (with Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, and Anderson AC). Methods Mol. Biol. 2017; 1529:291-306. PMID: 27914058
    • [PDF ]
  • Algorithms for protein design (with P. Gainza and H. Nisonoff). Current Opinion in Structural Biology. 2016: (39):16-26.
    • [PDF, PDF at Elsvier, At journal]
  • Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env (with Do Kwon Y, Pancera M, Acharya P, Georgiev IS, Crooks ET, Gorman J, Joyce MG, Guttman M, Ma X, Narpala S, Soto C, Terry DS, Yang Y, Zhou T, Ahlsen G, Bailer RT, Chambers M, Chuang GY, Doria-Rose NA, Druz A, Hallen MA, Harned A, Kirys T, Louder MK, O'Dell S, Ofek G, Osawa K, Prabhakaran M, Sastry M, Stewart-Jones GB, Stuckey J, Thomas PV, Tittley T, Williams C, Zhang B, Zhao H, Zhou Z, Lee LK, Zolla-Pazner S, Baxa U, Schon A, Freire E, Shapiro L, Lee KK, Arthos J, Munro JB, Blanchard SC, Mothes W, Binley JM, McDermott AB, Mascola JR, and Kwong PD). Nature Structural Molecular Biology. 2015; (22): 522-531. doi: 10.1038/nsmb.3051. PMID: 26098315
    • [Abstract, PDF]
  • Systematic solution to homo-oligomeric structures determined by NMR, (with J. Martin and P. Zhou). Proteins 2015; 83(4):651-661. Cover Article.
  • Protein Design Algorithms Predict Viable Resistance to an Experimental Antifolate (with S. Reeve, P. Gainza, K. Frey, I. Georgiev, and A. Anderson). Proceedings of the National Academy of Sciences, U.S.A. (PNAS). 2015; doi: 10.1073/pnas.1411548112
  • Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo (with R. Rudicell, Y. Kwon, S.Y. Ko, A. Pegu, M. Louder, I. Georgiev, X. Wu, J. Zhu, J. Boyington, X. Chen, W. Shi, Z. Yang, N. Doria-Rose, K. McKee, S. O'Dell, S. Schmidt, G.Y. Chuang, A. Druz, C. Soto, Y. Yang, B. Zhang, T. Zhou, J.P. Todd, K. Lloyd, J. Eudailey, K. Roberts, R. Bailer, J. Ledgerwood, NISC Comparative Sequencing Program, J. Mullikin, L. Shapiro, R. Koup, B. Graham, M. Nason, M. Connors, B. Haynes, S. Rao, M. Roederer, P. Kwong, J. Mascola, and G. Nabel). Journal of Virology 2014; 88(21):12669-82.
  • Structure of an HIV-1 Neutralizing Antibody Target: A Lipid Bound gp41 Envelope Membrane Proximal Region Trimer (with P. Reardon, H. Sage, D. Moses, J. Martin, A. Munir, B. Haynes, and L. Spicer). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2014; 111(4):1391-6.
    [Read the open-access PDF (PNAS website);
    View the structure: PDB Deposition 2m7w, NMR Solution Structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41, (with J. Martin, P. Reardon, H. Sage, D. Moses, A. Munir, B. Haynes, L. Spicer).]
  • Design of Epitope-Specific Probes for Sera Analysis and Antibody Isolation (with I. Georgiev, P. Acharya, S. Schmidt, Y. Li, D. Wycuff, G. Ofek, N. Doria-Rose, T. Luongo, Y, Yang, T. Zhou, J. Mascola, P. Kwong). Retrovirology 2012; 9(Suppl.2):P50. From AIDS Vaccine. Boston, MA. Sep. 9-12 (2012).
  • Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
    • [Abstract, PDF]
  • Predicting resistance mutations using protein design algorithms (with K. Frey, I. Georgiev, and A. Anderson). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2010; 107(31):13707-12. PubMed PMID: 20643959.
    • [Abstract, Full text, PDF, PDB Structures: 3GL4, 3F0Q]
  • High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations, (with J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, and P. Zhou). Journal of Biomolecular NMR 2009; 45(3):265-281. PMID: 19711185
    • [PDF, Supplementary Materials, PDB Structure 2KIQ]
  • Computational Structure-Based Redesign of Enzyme Activity (with C. Chen, I. Georgiev, and A. Anderson). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2009; 106(10):3764-3769.
    • [PDF, Supporting Information, Open access article, Abstract]
  • Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints (with J. Martin). Progress in NMR Spectroscopy 2009; 55(2):101-127.
    • [PDF, Full text at Jounal Website]
  • "Allosteric Inhibition of the Protein-Protein Interaction Between the Leukemia-Associated Proteins RUNX1 and CBFβ" (with R. Lilien and M. Sridharan) Chemistry & Biology 2007; 14(10):1186-1197.
    • [Medline, PDF, Supplementary material, PDB structure model, Cover article, Caption, Cover (PDF)]
  • Redesigning the PheA Domain of Gramicidin Synthetase Leads to a New Understanding of the Enzyme's Mechanism and Selectivity (with B. Stevens, R. Lilien, I. Georgiev, and A. Anderson). Biochemistry 2006; 45 (51):15495-15504.
    • [Medline, PDF, Abstract]
  • Structure Determination of Symmetric Homo-oligomers by a Complete Search of Symmetry Configuration Space Using NMR Restraints and van der Waals Packing (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg). Proteins 2006; 65(1):203-219.
    • [Medline, HTML, PDF, Supplementary materials, PDB Structure 2HYN]
  • A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
    • [Medline, PDF]
  • Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.
    • [Medline, PDF, Full text (at JBC), PDB Structure 1QZF]
  • The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Eukaryotic Microbiology 2003; 50(6):555-556. Cover article.
    • [Medline, PDF, Cover illustration]

• Neuroscience and Nanotechnology

  • Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches (with K. Hamaguchi, K. Tschida, I. Yoon, and R. Mooney). eLife 2014; 3:e01833. http://dx.doi.org/10.7554/eLife.01833
  • Intracellular neural recording with pure carbon nanotube probes (with I. Yoon, K. Hamaguchi, I. Borzenets, G. Finkelstein, and R. Mooney). PLoS One 8(6):e65715 (2013)
    • [Summary, PDF]
  • Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording (with I. Borzenets, I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of Applied Physics 2012; 111(7):74703-747036. doi: 10.1063/1.3702802.
    • [Summary, PDF]

• Protein Structures Gallery

  
  

  Selected Protein Structures We Have Deposited:

  • Crystal Structure of E. coli LptA in complex with Murgantia histrionica Thanatin (with K. Huynh, A. Kibrom and P. Zhou). PDB ID: 8GAL.
  • Crystal Structure of E. coli LptA in complex with Chinavia Ubica Thanatin (with K. Huynh, A. Kibrom and P. Zhou). PDB ID: 8GAK
  • Crystal Structure of E. coli LptA in complex with Podisus maculiventris Thanatin (with K. Huynh, A. Kibrom and P. Zhou). PDB ID: 8GAJ
  • Inhibitor R-27 in complex with Staph. aureus DHFR and tricyclic-NADPH (tNADPH) (with S. Reeve, S. Wang, and D. Wright). PDB ID: 7T7S.
  • Inhibitor R-27 in complex with Staph. aureus DHFR and α-NADPH (with S. Reeve, S. Wang, and D. Wright). PDB ID: 7T7Q.
  • Independently verified structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41, (with J. Martin, P. Reardon, H. Sage, D. Moses, A. Munir, B. Haynes, and L. Spicer) PDB ID: 2m7w .
  • Solution structure of the FF Domain 2 of human transcription elongation factor CA150, (with M. Zeng, C. Tripathy, J. Boyles, A. Yan, and P. Zhou), PDB ID: 2KIQ (2009).
  • Complete ensemble of NMR structures of Unphosphorylated Human Phospholamban Pentamer, (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg), PDB ID: 2HYN.
  • Crystal structure of Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) from Cryptosporidium hominis, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson), PDB ID: 1QZF.
  • Search PDB (NCBI/NLM) for all protein structures (circa 29) reported in our papers (NMR, X-ray, Cryo-EM)

• Algorithms in Structural Molecular Biology and Computational Chemistry

  • DexDesign: an osprey-based algorithm for designing de novo D-peptide inhibitors. (with N. Guerin, H. Childs and P. Zhou). Protein Engineering, Design, and Selection. 2024; 37:gzae007. doi: 10.1093/protein/gzae007. PMID: 38757573
    • [PDF]
  • DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors (with N. Guerin, H. Childs, and P. Zhou). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Boston. (April 29-May 2, 2024).
    In Lecture Notes in Computer Science 14758, Springer (Cham, Schweizerische Eidgenossenschaft) pp. 336-249.
  • RESISTOR: A New OSPREY Module to Predict Resistance Mutations (with N. Guerin and T. Kaserer). Journal of Computational Biology (Accepted, In press) 2022.
  • RESISTOR: An algorithm for predicting resistance mutations using Pareto optimization over multistate protein design and mutational signatures (with N. Guerin and T. Kaserer). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego. (May 22-25, 2022). In Research in Computational Molecular Biology, RECOMB 2022, Lecture Notes in Computer Science, vol. 13278. Springer (Cham, Schweizerische Eidgenossenschaft). pp. 387-389.
    • [html, pdf]
  • Minimization-Aware Recursive K* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape (with J. Jou, G. Holt, and A. Lowegard).
    • Journal of Computational Biology 2020; 27(4): 550-564, doi: 10.1089/cmb.2019.0315. [PDF]
    • Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC. (May 5-8, 2018). Springer Nature Switzerland AG (2019) RECOMB 2019, Lecture Notes in Bioinformatics (LNBI) 11467, pp. 101–119. [PDF, Supporting Material ]
  • Protein Design by Provable Algorithms (with M. Hallen). Communications of the ACM, 2019; 61(10): 76-84. DOI: 10.1145/3338124.
    • [PDF, html, video]

    Protein Design by Provable Algorithms (in Comm. ACM, 2019).

  • OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features. (with M. Hallen, J. Martin, et al).
    Journal of Computational Chemistry 2018; 39(30): 2494-2507 Cover article.
    Available here:
    [Journal of Computational Chemistry].
    Cover Image (Osprey)
    [PDF of paper]
    
  • Minimal NMR distance information for rigidity of protein graphs (with C. Lavor, L. Liberti, B. Worley, B. Bardiaux, T. Malliavin, and M. Nilges). Discrete Applied Mathematics 2019; 256: 91-104.
  • CATS (Coordinates of Atoms by Taylor Series): Protein design with backbone flexibility in all locally feasible directions (with M. Hallen). Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Prague (July, 2017).
    Journal version:
    Bioinformatics (2017) 33 (14): i5-i12.
    DOI: https://doi.org/10.1093/bioinformatics/btx277
    • [Abstract, HTML, PDF]
  • BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces (with A. Ojewole, J. Jou, and V. Fowler). Journal of Computational Biology 2018; 25(7): 726–739.
    • [Abstract, PDF, Supporting Material]
    
    
    This journal paper is based on our RECOMB (2017) conference paper:
    
    BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces (with A. Ojewole, J. Jou, and V. Fowler). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Hong Kong. (May 3-7, 2017). In: Research in Computational Molecular Biology, Lecture Notes in Computer Science (LNCS), Springer-Verlag (Berlin) vol. 10229, pp. 157-172.
    • [PDF here, SM; Abstract & PDF at Springer ]
    
    
  • LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency (with M. Hallen and J. Jou). Journal of Computational Biology 2016 Sep 28. PMID: 27681371
    The accepted manuscript has higher resolution figures than the published PDF:
    [ published journal PDF, SI, Accepted MS]

    This journal paper is a revised paper based on the earlier Conference version:

    LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency (with M. Hallen and J. Jou). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Los Angeles, CA, April, 2016. In Research in Computational Molecular Biology, Lecture Notes in Bioinformatics (LNBI), Springer-Verlag (Berlin), Volume 9649, 2016, pp. 122-136.

  • COMETS (Constrained Optimization of Multistate Energies by Tree Search): A provable and efficient protein design algorithm to optimize binding affinity and specificity with respect to sequence (with M. Hallen). Journal of Computational Biology 2015 23(5):311-21. doi: 10.1089/cmb.2015.0188. Epub 2016 Jan 13..
    • [PDF, SI]

    This journal paper is a revised paper based on the earlier Conference version:

    COMETS (Constrained Optimization of Multistate Energies by Tree Search): A provable and efficient algorithm to optimize binding affinity and specificity with respect to sequence (with M. Hallen). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Warsaw, April 12-15, 2015. In Research in Computational Molecular Biology Lecture Notes in Computer Science, Springer-Verlag (Berlin), Volume 9029, 2015, pp 122-135.

  • A compact representation of continuous energy surfaces for more efficient protein design (with M. Hallen and P. Gainza). Journal of Chemical Theory and Computation. 2015; 11(5):2292-2306.
    • [PDF, Abstract]
  • Parallel Computational Protein Design (with Zhou Y and Zeng J.) Methods Mol Biol. 2017;1529:265-277. PMID: 27914056
  • BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design (with J. Jou, S. Jain, and I. Georgiev). Journal of Computational Biology 2015 doi: 10.1089/cmb.2017.0267. .
    • [PDF, SI]

    This journal paper is a revised paper based on the earlier Conference version:

    BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design (with J. Jou, S. Jain, and I. Georgiev). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Warsaw, April 12-15, 2015. In Research in Computational Molecular Biology Lecture Notes in Computer Science, Springer-Verlag (Berlin), Volume 9029, 2015, pp 154-166.

  • Fast search algorithms for Computational Protein Design (with S. Traore, K. Roberts, D. Allouche, I. Andre, T. Schiex, and S. Barbe). Journal of Computational Chemistry 2016; 37(12):1048-58. doi: 10.1002/jcc.24290. Epub 2016 Feb 2. Cover Article.
    • [Abstract, PDF, SI]
  • Fast Gap-Free Enumeration of Conformations and Sequences for Protein Design (with K. E. Roberts, P. Gainza, and M. A. Hallen). Proteins (2015) doi: 10.1002/prot.24870 volume 83 issue 10 pages 1859-1877.
    • [Abstract, PDF]
  • Improved Energy Bound Accuracy Enhances the Efficiency of Continuous Protein Design (with K. Roberts). Proteins: Structure, Function, and Bioinformatics. 2015; 83(6):1151-64.
    • [Abstract, PDF]
  • An efficient parallel algorithm for accelerating computational protein design (with Y. Zhou, W. Xu, and J Zeng). Bioinformatics. 2014 Jun 15;30(12):i255-i263. Proceedings of ISMB, Boston, MA. doi: 10.1093/bioinformatics/btu264.
    • [HTML, PDF]
  • "OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms" (with P. Gainza, K. Roberts, I. Georgiev, R. Lilien, D. Keedy, C.-Y. Chen, F. Reza, A. Anderson, D. Richardson, and J. S. Richardson). Methods in Enzymology 2013; 523:87-107
    • [Abstract, PDF]
  • "Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data" (with H. Chandola and C. Bailey-Kellogg). Proceedings of the 4^th ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM BCB). Washington, DC. September, 2013. ACM Press. pp. 171-180.
    • [PDF]
  • "Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure" (with C. Tripathy, A. Yan, and P. Zhou). Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Beijing, China (2013). In: Research in Computational Molecular Biology, Lecture Notes in Computer Science (LNBI), Springer-Verlag (Berlin), Volume 7821 (2013). pp. 271-284.
    • [ PDF, Supplementary Material]
  • The Role of Local Backrub Motions in Evolved and Designed Mutations (with D. Keedy, I. Georgiev, E. Triplett, D. Richardson, and J. Richardson). PLoS Computational Biology 2012; 8(8): e1002629. doi:10.1371/journal.pcbi.1002629.
    • [Abstract, Open access at Journal, PDF]
  • "HASH: a Program to Accurately Predict Protein Hα (H-alpha) Shifts from Neighboring Backbone Shifts" (with J. Zeng, and P. Zhou). Journal of Biomolecular NMR 2012; Dec 16.
    • [PDF]
  • "Protein Design using Continuous Rotamers" (with P. Gainza and K. Roberts). PLoS Computational Biology (2012) 8(1): e1002335. doi:10.1371/journal.pcbi.1002335.
    • [Open access at the Journal, PDF ]
  • Dead-End Elimination with Perturbations (`DEEPer'): A provable protein design algorithm with continuous sidechain and backbone flexibility (with M. Hallen and D. Keedy). Proteins 2013; 80(1):18-39. DOI: 10.1002/prot.24150
    • [PDF, Abstract]
  • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). Cover Article.
    Proteins: Structure, Function, and Bioinformatics. Volume 80, Issue 2, pages 433-453, 2012. Journal online: DOI: 10.1002/prot.23207
    • [PDF, Abstract, Supplementary Information (SI), Cover (large, PNG)]
  • Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data, (with J. Zeng and P. Zhou). Journal of Biomolecular NMR 2011: 45(3):265-281.
    • [PDF]
  • A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers (with J. Martin, A. Yan, C Bailey-Kellogg, and P. Zhou). Protein Science 20(6):970-985 (2011) Mar 16. doi: 10.1002/pro.620. PMID: 21413097
    • [PDF]
  • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). Journal of Computational Biology 2011; 18(11):1507-23.
    • [PDF]
  • NMR Structural Inference of Symmetric Homo-Oligomers (with H. Chandola, A. Yan, S. Potluri, and C. Bailey-Kellogg). Journal of Computational Biology 2011; 18(12):1757-75. PMID: 21718128.
    • [PDF]
  • A Bayesian Approach for Determining Protein Side-chain Rotamer Conformations using Unassigned NOE Data (with J. Zeng, K. Roberts, and P. Zhou). Journal of Computational Biology 2011; 18(11):1661-79.

  • RECOMB 2011 papers

    • Design of protein-protein interactions with a novel ensemble-based scoring algorithm (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 361-376 (2011), DOI: 10.1007/978-3-642-20036-6
      • [PDF, Link to Proceedings]
    • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 222-237 (2011), DOI: 10.1007/978-3-642-20036-6.
    • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 483-498 (2011), DOI: 10.1007/978-3-642-20036-6
    • A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data (with J. Zeng, K. Roberts, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 563-578 (2011), DOI: 10.1007/978-3-642-20036-6

  • A Markov Random Field Framework for Protein Side-Chain Resonance Assignment (with J. Zeng and P. Zhou). International Conference on Research in Computational Molecular Biology (RECOMB), Lisbon, Portugal. April/August, 2010. In Lecture Notes in Computer Science, Springer (Berlin) Volume LNBI 6044/2010, pp. 550-570. ISBN 978-3-642-12682-6.
  • Algorithms and Analytic Solutions using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR (with A. Yershova, C. Tripathy, and P. Zhou), Workshop on the Algorithmic Foundations of Robotics (WAFR), Singapore (2010).
  • OSPREY User Manual (with I. Georgiev). Available online: www.cs.duke.edu/donaldlab/software.php (2009).
  • NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments (with S. Apaydin, B. Catay, and N. Patrick). The Computer Journal 2011; 54:708-716. Appeared Online in (Summer, 2010). doi:10.1093/comjnl/bxp120.
    An earlier conference version of paper in: IEEE 24th International Symposium on Computer and Information Science (ISCIS). Cyprus, 14-16 September 2009.
  • Algorithm for Backrub Motions in Protein Design (with I. Georgiev, D. Keedy, J. Richardson, and D. Richardson). Bioinformatics 2008; 4(13):i196-i204. Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto CA (July, 2008)
    • [PDF, Open access]
  • Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg). In Algorithmic Foundation of Robotics VII. Springer Tracts in Advanced Robotics (vol. 47), Ed. S. Akella et al. Springer-Verlag (Berlin) 2008 pp. 335-340.
  • A Hausdorff-Based NOE Assignment Algorithm Using Protein Backbone Determined from Residual Dipolar Couplings and Rotamer Patterns, (with J. Zeng, C. Tripathy, and P. Zhou). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2008) pp. 169-181.
    • [PDF]
  • Structure-Based Protein NMR Assignments using Native Structural Ensembles (with S. Apaydin and V. Conitzer). Journal of Biomolecular NMR 2008; 40(4):263-276. PMID: 18365752.
    • [Medline, PDF]
  • The Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles (with I. Georgiev and R. Lilien). Journal of Computational Chemistry 2008;29(10):1527-42. PMID: 1829329
    • [Medline, PDF]
  • Dead-End Elimination with Backbone Flexibility (with I. Georgiev). Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria: July 21-25, 2007. Appears in in Bioinformatics 2007; 23(13):i185-i195.
    • [Medline, PDF, Open Access]
  • A Complete Algorithm to Resolve Ambiguity for Inter-subunit NOE Assignment in Structure Determination of Symmetric Homo-oligomers (with S. Potluri, A. Yan, and C. Bailey-Kellogg). Protein Science 2007; 16(1):69-81.
    • [Medline, PDF]
  • A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data (with L. Wang and R. Mettu). Journal of Computational Biology 2006; 13(7): 1276-1288.
    • [Medline, PDF]
  • A Data-Driven, Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins (with L. Wang). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2006) Pages 67-78. ISBN 1-86094-700-X.
    • Winner of Best Paper Award.
    • [Medline, PDF, Amazon, Imperial College Press]
  • Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End Elimination, with Application to Protein Design (with I. Georgiev and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil (2006). Bioinformatics 2006; 22(14):e174-183.
    • [Medline, PDF, Open Access]
  • A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles, (with I. Georgiev and R. Lilien). Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy (April 2-5, 2006). In Springer Berlin, Lecture Notes in Computer Science, RECOMB 2006, LNBI 3909, pp. 530-545, 2006.
    • [Medline, PDF]
  • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
    • [Medline, PDF, Erratum ]
    • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
  • L. Wang and B. R. Donald. An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 189-202.
    • [Medline, PDF ]
  • L. Wang, R. Mettu, and B. R. Donald. An Algebraic Geometry Approach to Protein Backbone Structure Determination from NMR Data. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 235-246.
    • [Medline, PDF ]
  • High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data (with R. Mettu and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI (2005).
  • A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
    • [Medline, PDF]
  • Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure (with L. Wang), Journal of Biomolecular NMR 2004; 29(3):223-242.
    • [Medline, PDF, full text (at JBN)]
  • An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments (with C. Langmead). Journal of Biomolecular NMR 2004; 29(2):111-138.
    • [Medline, PDF, Full text (at JBN) ]
  • A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme (with R. Lilien, B. Stevens, and A. Anderson). Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego (March 27-31, 2004) pp. 46-57.
    • [PDF]
  • A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry (with R. Lilien, C. Bailey-Kellogg, and A. Anderson). Acta Crystallographica D: Biological Crystallography 2004; D60, 1057-1067.
    • [Medline, PDF, Full text (at IUCR)]
  • Symmetry, Goniometers and RDCs (with A. Yan). Tutorial, Donald Laboratory, Departments of Computer Science and Chemistry, Dartmouth College, Hanover NH (2004).
    • [PDF]
  • High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment (with C. Langmead). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA, (August, 2004) pp. 278-289.
    • [Medline, PDF]
  • Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings (with L. Wang). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA (August, 2004) pp. 319-330.
    • [Medline, PDF]

    	Nuclear Vector Replacement.

  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Journal of Computational Biology 2004; 11(2--3):277-298.
    • [Medline, PDF]
  • A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology (with A. Yan and C. Langmead). The International Journal of Robotics Research Special Issue on Robotics Techniques Applied to Computational Biology, 2005; (29)(2-3):165-182.
    • [PDF]
  • "3D Structural Homology Detection via Unassigned Residual Dipolar Couplings," (with C. Langmead) Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 209-217. ISBN 0-7695-2000-6.
    • [Medline, PDF]
  • "An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings," (with L. Wang, R. Mettu, and R.Lilien), Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 611-612. ISBN 0-7695-2000-6.
    • Winner of Best Poster Award.
  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proc. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.
    • [PDF]
  • " Ensembles of active site conformations allow structure-based redesign and drug design," (with A. Anderson, R. Lilien and V. Popov), 225^th American Chemical Society National Meeting, March 23-28, 2003. New Orleans, LA.
  • "Modeling Protein Flexibility for Structure-Based Active Site Redesign", (with R. Lilien and A. Anderson), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). In Currents in Computational Molecular Biology, 2002 (ed. L. Florea et al.) pp 122-123.
    • [ PDF]
  • "Modeling of Protein Flexibility for Computational Active Site Redesign," (with R. Lilien and A. Anderson) The 16th Annual National MD/PhD Conference, Given Institute, Aspen, Colorado, July 13-15, 2001.
  • "Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data" (with C. Langmead), Proceedings of The Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Montreal, April 22-25 (2001) pp. 164-175
    • [PDF]
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of Computational Biology, 8(1):19-36, 2001.
    • [Medline, PDF]
      
    • [The figures look better in this pdfLaTeX reprint]
  • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Journal of Computational Biology, 7(3-4) (2000) pp. 537-558.
    • [Medline, PDF]
    • [The figures look better in this pdfLaTeX reprint]
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) Proc. the 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA (pp. 13-24).
    • [Medline]
  • "Computational Screening Studies for Core-Binding Factor Beta (CBFβ): Use of Multiple Conformations to Model Receptor Flexibility," (with R. Lilien, M. Sridharan, X. Huang, and J. Bushweller), 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA.
  • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB'2000), Tokyo, Japan, April 8-11, 2000, pp. 33-45.
  
  

• Review/Survey Articles

  • Algorithms for protein design (with P. Gainza and H. Nisonoff). Current Opinion in Structural Biology. 2016: (39):16-26.
    • [PDF, PDF at Elsvier, At journal]
  • Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints (with J. Martin). Progress in NMR Spectroscopy 2009; 55(2):101-127.
    • [PDF, Full text at Jounal Website]
  • Algorithmic Challenges in Structural Molecular Biology and Proteomics, Plenary lecture at WAFR, Utrecht/Zeist, The Netherlands. July 11-13, 2004. Appears in Springer Tracts in Advanced Robotics (vol. 17), Springer (Berlin) 2005, pp. 1-10.
    • [PDF, HTML]
  • "Physical Geometric Algorithms for Structural Molecular Biology" (with C. Bailey-Kellogg, J. Kelley, and R. Lilien) invited paper at the Special Session on Computational Biology & Chemistry, Proc. International Conference on Robotics and Automation (2001), Seoul, Korea, pp. 940-947.
    • [PostScript, PDF]

• Robotics

  • MicroElectroMechanical Systems (MEMS), Nanoscience, and Microrobotics

    Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with many videos describing our MEMS, Microrobotics, and Nanoscience research.

    Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

    • Intracellular neural recording with pure carbon nanotube probes (with I. Yoon, K. Hamaguchi, I. Borzenets, G. Finkelstein, and R. Mooney). PLoS One 8(6):e65715 (2013)
      • [Summary, PDF]
    • Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots (with C. Levey, C. McGray, I. Paprotny, and D. Rus). International Journal of Robotics Research 2013; 32(2): 218-246.
      • [Abstract, PDF]
    • Turning-rate Selective Control: A New Method for Independent Control of Stress-engineered MEMS Microrobots (with C. Levey and I. Paprotny). Proceedings of Robotics: Science and Systems Conference (RSS), University of Sydney, Sydney, NSW, Australia. July 9-13, 2012 (In press).
      • [Abstract, PDF]
    • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
      • [PDF]
    • Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording (with I. Borzenets, I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of Applied Physics 2012; 111(7):74703-747036. doi: 10.1063/1.3702802.
      • [Summary, PDF]
    • Simultaneous Control of Multiple MEMS Microrobots (with C. Levey, I. Paprotny, and D. Rus). Proceedings of the Eighth International Workshop on the Algorithmic Foundations of Robotics (WAFR), Guanajuato, Mexico, December 7-9, 2008.
      Book chapter version (final) appears in: Springer Tracts on Advanced Robotics, 57, Springer-Verlag (Berlin), (2010), pp. 69-84.
      • [PDF, Supplementary Material]
    • Planar Microassembly by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Journal of Microelectromechanical Systems 2008; 17(4): 789-808.
      • [PDF, Video, Supporting Material, Ballet video, Youtube videos, Movies ]
    • Assembly of Planar Structures by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Hilton Head Workshop: A Solid-State Sensors, Actuators and Microsystems Workshop pp. 202-207. June 1-2, 2008, Hilton Head, SC.
      • [PDF, Video, Supporting Material, Ballet video, Youtube videos]
    • A Steerable, Untethered MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). In Robotics Research, Springer Tracks in Advanced Robotics 28, ed. S. Thrun, et al., Springer-Verlag (Berlin) 2007, pp. 337-356.
    • An Untethered, Electrostatic, Globally-Controllable MEMS Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). Journal of Microelectromechanical Systems, 2006; 15(1):1-15.
      • [PDF, Full text at IEEE, Supplementary Material (Videos)]
    • A Steerable, Untethered, 250 x 60 µm MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). 12th International Symposium of Robotics Research (ISRR), October 12-15, 2005, San Francisco, CA.
    • Power Delivery and Locomotion of Untethered Micro-Actuators (with C. Levey, C. McGray, D. Rus, and M. Sinclair). Journal of Microelectromechanical Systems 2003; 10(6):947-959.
      • [PDF, Movies]
    • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair). in Robotics Research eds. P. Dario and R. Chatila. Springer-Verlag (London) 2005, pp.502--516.
    • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair) 11^th International Symposium of Robotics Research (ISRR), October 19-22, 2003, Siena, Italy.
    • Power Delivery and Locomotion of Untethered Micro-Actuators, (with C. Levey, C. McGray, D. Rus, and M. Sinclair) IEEE MEMS (Proc. IEEE International Conference on Micro Electro Mechanical Systems), Kyoto, Japan, January 19-23, 2003. pp.124-129.
      • [PDF, Movies]
    • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE Transactions on Robotics and Automation, 16(2), April 2000, pp. 157-170.
      • [Abstract, PDF]

    • Fully Programmable MEMS Ciliary Actuator Arrays for Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G.Kovacs), the IEEE International Conference on Robotics and Automation (ICRA) San Francisco (April, 2000) pp. 1101-1108.
    • Sensorless Manipulation Algorithms Using a Vibrating Surface, (with K.-F. Böhringer, V. Bhatt, and K. Goldberg) Algorithmica 26(3/4), March/April (2000) pp. 389-429.

    • CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) Journal of Microelectromechanical Systems, vol. 8, No. 4 (Dec. 1999), pp. 483-496.
      • [PDF] B&W version of published paper
    • "A Single Universal Force Field Can Uniquely Pose Any Part Up To Symmetry," (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki) 9th International Symposium of Robotics Research (ISRR) Snowbird, Utah October 9-12 (1999).
      • [PDF]
    • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000):
      1. CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs).
      2. A Distributed, Universal Device for Planar Parts Feeding: Unique Part Orientation in Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki).
      3. Constrained Prehensile Manipulation: Distributed Manipulation with Ropes (with L. Gariepy and D. Rus).
    • CMOS Integrated Organic Ciliary Actuator Array as a General-Purpose Micromanipulation Tool (with J. Suh, B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation, (Detroit) May 11, 1999.
    • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation (Detroit) May 11, 1999.
    • Algorithmic MEMS, (with K.-F. Böhringer), Invited lecture at the Third International Workshop on the Algorithmic Foundations of Robotics (WAFR), Houston, TX (March, 1998). Book version: In Robotics: The Algorithmic Perspective, ed. P. Agarwal et al., A. K. Peters, Natick, MA (1998). pp. 1-20.
    • Computational Methods for the Design and Control of MEMS Micromanipulator Arrays (with K.-F. Böhringer, G. Kovacs, N. MacDonald, and J. Suh) IEEE Computational Science and Engineering, Vol. 4, No. 1. Special Issue on Computational MEMS (Jan-March 1997). pp. 17-29.
      • [PDF]
    • On The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Discrete and Computational Geometry, vol. 22 (1999), pp. 269-285.
    • Programmable Vector Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders, [TR FTP] (with K.-F. Böhringer, and N. C. MacDonald), (International Journal of Robotics Research). vol. 18(2), pp. 168-200 (1999).
      • Galleys from IJRR: [PDF]
    • Micro Contacts and Micro Manipulation with MEMS Actuator Arrays, (with K.-F. Böhringer IEEE International Conference on Robotics and Automation, Workshop on Modeling, Contact Analysis, and Simulation of Mechanical Systems in Robotics and Manufacturing, (Belgium, 1998).
    • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
    • Vector Fields for Task-Level Distributed Manipulation: Experiments with Organic Micro Actuator Arrays [TR FTP], (with K.-F. Böhringer, J. Suh, and G. Kovacs) in Proc. IEEE International Conference on Robotics and Automation, Albuquerque, NM (1997). pp 1779-1786.
    • The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields [TR FTP], (with K.-F. Böhringer, and D. Halperin) 13th Proc. ACM Symposium on Computational Geometry, Nice, France (1997) pp. 457-459.
    • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
    • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Single-Crystal Silicon Actuator Arrays for Micro Manipulation Tasks [TR FTP], IEEE Workshop on Micro Electro Mechanical Systems (MEMS), San Diego, California (February 1996).
    • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Classification and Lower Bounds for MEMS Arrays and Vibratory Parts Feeders: What Programmable Vector Fields Can (and Cannot) Do, IEEE International Conference on Robotics and Automation (ICRA), Minneapolis, Minnesota (April 1996).
    • Distributed Robotic Manipulation: Experiments in Minimalism [TR FTP], in International Symposium on Experimental Robotics, (ISER) Stanford, CA (1995). Appears in: in Experimental Robotics IV, Lecture Notes in Control and Information Sciences 223, ed. O. Khatib et al., Springer Verlag (Berlin) 1997 pp. 11-25.
    • Sensorless Manipulation Using Massively Parallel Micro-fabricated Actuator Arrays [TR FTP] (with K.-F. Böhringer, R. Mihailovich, and Noel C. MacDonald), Proc. IEEE International Conference on Robotics and Automation, San Diego, CA (May, 1994).
      A demo and more detailed explanation.
    • A Theory of Manipulation and Control for Microfabricated Actuator Arrays, Proceedings of the IEEE Workshop on Micro Electro Mechanical Systems (MEMS), Oiso, Japan (January 1994).
      • [PDF]

  • Mobile Robotics

    Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with many videos describing our mobile robotics research.

    Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

    • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
      • [PDF]
    • Distributed Manipulation of Multiple Objects Using Ropes, (with L. Gariepy and D. Rus), Proc. IEEE International Conference on Robotics and Automation (ICRA), San Francisco (April, 2000) pp. 450-457.
    • Practical Mobile Robot Self-Localization (with J. Howell) Proceedings, International Conference on Robotics and Automation, San Francisco, CA, April 24-28, 2000. pp. 3485-3492.

      Movie, 4:30, Quicktime w/Sorenson codec, max 250 kb/s (42MB)	mapmaking-movie-5.250kbit.mov
      Movie, 4:30, Quicktime w/Sorenson codec, max 100 kb/s (26MB)	mapmaking-movie-5.100kbit.mov
      The paper (Gzipped PostScript) (0.8 MB)	ICRA'2000 paper

    • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.
    • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.
    • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000).
    • Experiments in Constrained Prehensile Manipulation: Distributed Manipulation with Ropes, with Larry Gariepy and Daniela Rus, In Experimental Robotics VI, Lecture Notes in Control and Information Sciences, Vol. 250, eds. P. Corke, Springer-Verlag, (2000).

    • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
    • Information Invariants for Distributed Manipulation (with J. Jennings and D. Rus) in International Journal of Robotics Research, Vol. 16, No. 5 (1997). pp. 673-702.
      • Here are the galleys from MIT Press (7/14/97).
      • Technical Report (1994) [TR FTP]
      • [Movie]

    • B. R. Donald, J. Jennings, and D. Rus, Minimalism + Distribution = Supermodularity [TR FTP], Journal of Experimental and Theoretical Artificial Intelligence (JETAI), Special issue on Software Architectures for Hardware Agents; Vol. 9 No. 2-3 (1997) pp. 293-321.
      • [PDF]

    • . On Information Invariants in Robotics. Artificial Intelligence 72 (Jan, 1995) pp. 217-304.
      • [ Abstract, PDF, Accepted Manuscript ]

    • Cost-effective, Capable, and Configurable Multiple Robots: A Report to the ARPA ISAT Study Group, Summer, 1996 (with J. Jennings and D. Rus).
    • R.G. Brown and J.S. Jennings. A pusher/steerer model for strongly cooperative mobile robot cooperation. In IEEE/RSJ IROS, pages 562-568, 1995.
    • Moving Furniture with Teams of Automonous Mobile Robots [TR FTP], (with J. Jennings and D. Rus) in

      Proc. IEEE/Robotics Society of Japan International Workshop on Intelligent Robots and Systems, (IROS) Pittsburgh, PA (1995).

    • .
      Program Mobile Robots in Scheme (with J. Rees) Proc. IEEE International Conference on Robotics and Automation Nice, France (May, 1992), pp. 2681-2688.
      
      [PDF]
      Many people do not realize that the title of this paper is in the hortatory subjunctive mode. It should be read as:
      Program Mobile Robots in Scheme! Note the exclamation point.

    • Information Invariants for Distributed Manipulation [TR FTP] (with J. Jennings and D. Rus) in The First Workshop on the Algorithmic Foundations of Robotics, A. K. Peters, Boston, MA. ed. R. Wilson and J.-C.Latombe (1994).
      • [Movie]
    • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
    • Towards a Theory of Information Invariants for Cooperating Autonomous Mobile Robots, (with J. Jennings and D. Rus) International Symposium of Robotics Research (ISRR). Hidden Valley, PA (October 2, 1993).
    • Sensor Interpretation and Task-Directed Planning Using Perceptual Equivalence Classes (with J. Jennings). Proc. IEEE International Conference on Robotics and Automation, Sacramento, CA (April, 1991), pp. 190-197.
      • [PDF]

  • Motion Planning and Geometric Algorithms

    • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.

    • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.

    • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
    • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
    • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).

    • Kinodynamic Planning

      Here are 3 of our papers on Kinodynamic Planning:

    • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [PDF] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
      • [PDF]
      Other versions (Figures may look better in the TR):
      
      Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
      • [PDF]
    • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [PDF] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
      • [PDF]
      Other versions (Figures may look better in the TR):
      
      Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
      • [PDF]
    • Kinodynamic Motion Planning [PDF] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
      • [PDF]
      Other versions (Figures may look better in the TR):
      
      Kinodynamic Motion Planning - TR version [TR FTP] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
      • [PDF]

      
      

      A few papers before 1994:

    • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
    • ``The Motion of Planar Compliantly-Connected Rigid Bodies in Contact, with Applications to Automatic Fastening,'' B. R. Donald and D. Pai. International Journal of Robotics Research 12(4), August 1993, pp. 307-338.
      • [PDF]
    • ``Symbolic Methods for the Simulation of Planar Mechanical Systems in Design,'' B. R. Donald and D. Pai. in Symbolic and Numerical Computation for Artificial Intelligence, (ed. B. Donald et al.) Academic Press, Harcourt Jovanovich, (London: 1992), pp. 245-258.
    • Planning Multi-Step Error Detection and Recovery Strategies. International Journal of Robotics Research, 9(1), 1990. pp. 3-60.
      • [PDF]
    • Simplified Voronoi Diagrams (with J. Canny). Discrete and Computational Geometry 3:219-236 (1988).
      • [PDF]
    • A Geometric Approach to Error Detection and Recovery for Robot Motion Planning with Uncertainty, Artificial Intelligence, 1988: 37(1-3), pp. 223-271.
      • [PDF]
    • A Search Algorithm for Motion Planning with Six Degrees of Freedom, Artificial Intelligence 31(3), 1987. pp. 295-353.
      • [PDF]
    • For more older papers, please see here.

• Graphics, Haptics, Computer-Aided Architecture, and Animation

  Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with some videos describing our graphics and animation research. Some of our videos are copyrighted by the music publisher (because of the music) and therefore are here, here, or here, or here. Or Here (Siggraph 1990).

  Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

  • "Accessible Animation and Customizable Graphics via Simplicial Configuration Modeling" (with T. Ngo, D. Cutrell, J. Dana, L. Loeb, and S. Zhu), in Proc. ACM SIGGRAPH (New Orleans) July, 2000, pp. 403-410.
    • [PDF, Videos, other formats]
    
  • Using Haptic Vector Fields for Animation Motion Control (with F. Henle) Proc. IEEE Int. Conf. on Robotics and Automation (ICRA), San Francisco (April, 2000) pp. 3435-3442.
    • [PDF, Robot Aerobics video]
  • Prototyping Animation Motion Control with Haptic Programmable Force Fields, Workshop on "Motion Support in Virtual Prototyping," (with Fred Henle) Stanford, May 5-7, 1999.
  • System for Image Manipulation and Animation Using Embedded Constraint Graphics (with J. T. Ngo), U.S. Patent #5,933,150, issued August 3, 1999.
    • [PDF]

    

  • Real-Time Robot Motion Planning Using Rasterizing Computer Graphics Hardware, (with J. Lengyel, M. Reichert, and D. Greenberg), Proc. SIGGRAPH '90, Dallas, TX (Aug 1990), pp. 327-336.
    • [SIGGRAPH 1990 Video]
    • [ PDF, Movies, PostScript ]

  
  
  
  
  
  

  • Selected Manuals, Software Documentation, Technical Reports, and Design Exhibitions

    • The EIGHT Manual: An Introduction to Geometric Modelling and Three-Dimensional Graphics on the Lisp Machine. Working Paper 262, MIT Artificial Intelligence Laboratory, Cambridge, MA (1984); and Cornell Computer Science Department Technical Report TR 91-1186, Cornell University, Ithaca NY (1991).
      • [PDF]
      
    •  BUILDER: A Database and Display Program for Computer-aided Architectural Design. A system for representation and display of design problems in architecture and urban design. Laboratory for Computer Graphics and Spatial Analysis, Graduate School of Design, Harvard University. Cambridge, MA (1981).
      NB: The manual is mostly text with a few black-and-white images. Some nice color images from BUILDER can be found here.
      • [PDF, Color images from BUILDER, BUILDER Exhibitions]
    • BUILDER: A Database and Display Program for Computer-aided Architectural Design. Harvard Computer Graphics Conference, (Session 17, Architectural Practice) July 27, 1982. Cambridge, MA.
      • [Scanned 35 mm slides]
      
    • A Familiar Space in Two Dimensions: Piper Auditorium Computer-aided Design (CAD) Study (with Paul Stevenson Oles). Design Exhibition. Graduate School of Design, Harvard University (1982).
      • [Scanned renderings and images from exhibition]
    •  Alternative Methods of Language Creation. Documentation of the GLIB language maker for the LINGUIST language system. Laboratory for Computer Graphics and Spatial Analysis, Graduate School of Design, Harvard University. Cambridge, MA (1979).
      • [PDF]

• Computational Geometry

  • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). Cover Article.
    Proteins: Structure, Function, and Bioinformatics. Volume 80, Issue 2, pages 433-453, 2012. Journal online: DOI: 10.1002/prot.23207
    • [PDF, Abstract, Supplementary Information (SI), Cover (large, PNG)]
  • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). Journal of Computational Biology 2011; 18(11):1507-23.
    • [PDF]
  • A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers'' (with J. Martin, A. Yan, C Bailey-Kellogg, and P. Zhou). Protein Science 20(6):970-985 (2011) Mar 16. doi: 10.1002/pro.620. PMID: 21413097
    • [PDF]
  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proc. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.
    • [PDF]

  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.

  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE Transactions on Robotics and Automation, 16(2), April 2000, pp. 157-170.
  • "A Single Universal Force Field Can Uniquely Pose Any Part Up To Symmetry," (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki) 9th International Symposium of Robotics Research (ISRR) Snowbird, Utah October 9-12 (1999).
  • On The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Discrete and Computational Geometry, vol. 22 (1999), pp. 269-285.
  • Part Orientation with One or Two Stable Equilibria , (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), International Conference on Robotics and Automation, Workshop on Distributed Manipulation (Detroit) May 11, 1999.
  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields [TR FTP], (with K.-F. Böhringer, and D. Halperin) 13th Proc. ACM Symposium on Computational Geometry, Nice, France (1997) pp. 457-459.

  • Programmable Vector Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders, [TR FTP] (with K.-F. Böhringer, and N. C. MacDonald), (International Journal of Robotics Research, 1999) vol. 18(2) pp. 168-200.
    • Galleys from IJRR: [PDF]
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
  • . Kinodynamic Motion Planning [TR FTP] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
    • [PDF reprint]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • A Rational Rotation Method for Robust Geometric Algorithms, (with J. Canny and E. Ressler). Annual Symposium on Computational Geometry, Proceedings of the Eighth Annual Symposium on Computational Geometry, (1992) Berlin, Germany pp. 251-260.
  • Simplified Voronoi Diagrams (with J. Canny). Discrete and Computational Geometry 3:219-236 (1988).
    • [PDF]

• Prior to 1994

  • I started putting my papers on the Web around 1994. For books and papers before that, most are available at the publishers' web sites. I have added a few pre-1994 papers to the list above, after getting a lot of requests..

    The lab YouTube channel http://www.youtube.com/user/labdonald/videos, has many videos describing our research, starting around 1988.

    My C.V. (PDF) contains a list of publications, including a complete list those prior to 1994 (prior to 2015, actually).

  

  • Theses and Dissertations

    • S.M. Thesis MIT AI Lab, Local and Global Techniques for Motion Planning (1984), in two parts:
      • Motion Planning with Six Degrees of Freedom, AI Tech Report AI-TR-791, and
      • Hypothesizing Channels through Free-Space in Solving the Findpath Problem, AI Memo AI-TR-736
    • Ph.D. Thesis MIT AI Lab:
      • Error Detection and Recovery for Robot Motion Planning with Uncertainty (1987).
        A revised version was published by Springer as my first book at Cornell:

        Error Detection and Recovery in Robotics, Lecture Notes in Computer Science, Vol. 336, Springer-Verlag, New York (1989). 314 pp.
        ISBN 0387969098

      • [Download PDF eBook from Springer-Verlag, Order a soft copy]
      • [Cheaper soft copy, or here]

• Possums