Bruce Donald

Bruce Randall Donald
James B. Duke Professor

Professor of
              Computer Science
              Electrical Engineering

Duke University

Contact, Email, FAQ

Algorithms in Structural Molecular Biology,  MIT Press (2011)
Textbook (MIT Press).

Welcome to Bruce Donald's homepage. I am a Professor of Computer Science at Duke University, Professor of Mathematics, Professor of Chemistry, and Professor of Biochemistry in the Duke University Medical Center. I am also Professor of Electrical and Computer Engineering in the Duke Pratt School of Engineering.

My laboratory is part of the

We are grateful to our funders for their support.

You can browse my books and papers, learn about research in my laboratory, read about my lab in the news, or take my (not entirely?) Random Walk:
  1976-1980 Yale, B.A.
  1980-1984 Harvard, GSD
  1982-1987 MIT, Ph.D. in Computer Science
  1987-1998 Cornell Computer Science Department, Professor
  1994-1996 Stanford University, Sabbatical
  1995-1997 Interval Research Corporation
  1997-2006 Dartmouth, Professor
  2018-now  Ten63 Therapeutics, Founder
  2006-now  Duke, Professor.

Feel free to check out classes I teach.

Here are tips on using LaTeX for NIH grant applications, and seminars of interest for lab members.

Our lab has a YouTube channel.

I have a bit of fun stuff: you can check out my band, more music (MP3s), MEMS movies, robot movies, and other hacks.

    If you are interested in joining my laboratory, please read my brief FAQ.

    Bruce R. Donald
    Professor of Computer Science, Duke University
    Professor of Biochemistry, Duke University Medical Center
    P.O. Box 90129
    Department of Computer Science
    D101 Levine Science Research Center (LSRC)
    Research Drive
    Duke University
    Durham, NC 27708-0129 USA

    Please do not publish my e-mail address on any website or mailing list or book (yes, people have actually published books that are lists of scientists' email addresses). It will cause me to receive spam, since the address can be harvested by advertisers.
    It's my initials: `b' followed by `r' followed
by `d' `at' `cs' period `duke' period 'edu'.
    Phone: 919-660-6583

    Office: D212 Levine Science Research Center (LSRC)
    Donald Laboratory:
    Google maps; Duke Maps: LSRC, FFSC

    Et cette proposition est généralement vraie en toutes progressions et en tous nombres premiers; de quoi je vous envoierois la démonstration, si je n'appréhendois d'être trop long.

Cover Articles (See all)

Some of our papers (See all)

Drug Design

Broad spectrum inhibitors targeting methicillin-resistant clinical isolates of Staph. aureus

ACS Infectious Diseases (2019)
Preprint on BioRχiv

Combatting Leukemia:
RUNX1 and CBFβ Interaction Interupted.
Chemistry & Biology (2007).

Protein Structures Gallery

Structure of a membrane-associated MPER trimer from HIV-1 gp41

PDB id: 2m7w.

Solution structure of FF Domain 2 of human transcription elongation factor CA150.
PDB ID: 2KIQ (J. Biomol. NMR 2009)

Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis.
PDB ID: 1QZF (J. Biol. Chem.)

Complete ensemble of NMR structures of the unphosphorylated human cardiac phospholamban pentamer. PDB ID: 2HYN (Proteins, 2006)

Nanoscience and Microelectromechanical Systems

Independent Control of Stress-engineered MEMS Microrobots
Robotics: Systems and Science (2012)

Planar Microassembly by Parallel Actuation
of MEMS Microrobots.
Journal of Microelectromechanical Systems (2008).

Neuroscience, Microtechnology, and Nanotechnology

Auditory synapses to song premotor neurons
eLife (2014)

Intracellular Neural Recording with
Pure Carbon Nanotube Probes

PLoS (2013).

Microassembly by Microrobots

International Journal of Robotics Research (2013)

Carbon nanotube-based probes for scanning microscopy and neural recording

Journal of Applied Physics (2012).

Protein Design

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

PLoS Computational Biology (April, 2012).

Protein Design using Continuous Rotamers

PLoS Computational Biology (Jan, 2012).

The Role of Local Backrub Motions in Evolved and Designed Mutations

PLoS Computational Biology (August, 2012).

Cover Article

Protein loop closure using orientational
restraints from NMR data.
Proteins (2011)

Protein Design

DEEPer: A provable protein design algorithm with continuous sidechain and backbone flexibility

Proteins (July, 2012).

Design of Epitope-Specific Probes for Sera Analysis and Antibody Isolation

Retrovirology (2012).

OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms

Methods in Enzymology (2013)

Featured Research (See all)

Computational design of a tight binder to KRas, an “undruggable” cancer target

PLoS Computational Biology 2020.
Preprint on BioRχiv

Energy landscapes of inhibitors binding to
Cystic Fibrosis transmembrane conductance regulator
(CFTR)-Associated Ligand

Journal of Physical Chemistry B (2019)
local PDF

Broad spectrum inhibitors targeting methicillin-resistant clinical isolates of Staph. aureus

ACS Infectious Diseases (2019)
Preprint on BioRχiv

Communications of the ACM (2019).

Osprey has a Python interface and integrated GPU support

A convenient Python scripting interface and support for GPU acceleration allows designs to be completed far more quickly and easily (2020).

Continuous interdomain orientation distributions reveal components of binding thermodynamics

Journal of Molecular Biology (2018)

Featured Clinical Trials (See all)

Comment in The Lancet
A designed antibody from our Jour. Virology (2014) paper is currently in twelve clinical trials. Here are two: Identifier: NCT03015181
Safety and Pharmacokinetics of a Human Monoclonal Antibody, VRC07-523LS, Administered Intravenously or Subcutaneously
National Institutes of Health Clinical Center (2017)

Phase I study results in The Lancet. Identifier: NCT03387150
Evaluating the Safety and Serum Concentrations of a Human Monoclonal Antibody, VRC07-523LS, Administered in Multiple Doses and Routes

National Institutes of Health Clinical Center (2017)

Osprey 3.0


Open Source Protein REdesign for You, with Powerful New Features
Journal of Computational Chemistry (2018).
Cover article

[PDF, Accepted MS, Download Code]


Developing a Fluoride Riboswitch

East Chapel Hill High School iGEM Team (2017) &
ECHHS iGEM Team (2018)
Chloramphenicol acetyltransferase operon for an improved Fluoride Riboswitch as a Technology to Combat Excess Fluoride in Water

Recent Papers (See all)

Sublinear-Time Protein Design Algorithm to Optimize Binding Affinity and Stability over Large Sequence Spaces

JCB (2018)

CATS (Coordinates of Atoms by Taylor Series): Protein design with backbone flexibility in all locally feasible directions

ISMB & Bioinformatics (2017)

Algorithms for protein design
Curr Opin Struct Biol. (2016)

Nature Structural & Molecular Biology (2015)
Structure and conformational fixation
of mature ligand-free HIV Envelope Trimer

Protein Design Algorithms Predict Viable Resistance to an Experimental Antifolate
PNAS (2015)

Cover Article
Systematic solution to homoöligomeric structures determined by NMR
Proteins (2015)

An enhanced anti-HIV broadly neutralizing antibody
Journal of Virology (2014)

Structure of an HIV Neutralizing Antibody Target: A Lipid Bound gp41 Envelope Membrane Proximal Region Trimer.
PNAS (2014)

Protein Design

Predicting Resistance Mutations using Protein Design Algorithms.
PNAS (2010).

Computational Structure-Based Redesign of Enzyme Activity.
PNAS (2009).