Bruce Randall Donald

ORCID

Publication Activity (10 Years)

Years Active: 1985-2024
Publications (10 Years): 20

Top Venues

Publications

Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald
DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. RECOMB (2024)
Siyu Wang, Stephanie M. Reeve, Graham T. Holt, Adegoke A. Ojewole, Marcel S. Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G. Fowler, Dennis L. Wright, Bruce Randall Donald
Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. PLoS Comput. Biol. 18 (2) (2022)
Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. J. Comput. Biol. 27 (4) (2020)
Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke Ojewole, Bruce Randall Donald
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface. PLoS Comput. Biol. 16 (6) (2020)
Carlile Lavor, Leo Liberti, Bruce Randall Donald, Bradley Worley, Benjamin Bardiaux, Thérèse E. Malliavin, Michael Nilges
Minimal NMR distance information for rigidity of protein graphs. Discret. Appl. Math. 256 (2019)
Mark A. Hallen, Bruce Randall Donald
Protein design by provable algorithms. Commun. ACM 62 (10) (2019)
Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald
Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. RECOMB (2019)
Bruce Randall Donald
Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk). SoCG (2019)
Adegoke Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald
A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. J. Comput. Biol. 25 (7) (2018)
Mark A. Hallen, Bruce Randall Donald
Protein Design by Algorithm. CoRR (2018)
Mark A. Hallen, Jeffrey W. Martin, Adegoke Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou, Elizabeth Dowd, Bruce Randall Donald
OSPREY 3.0: Open-source protein redesign for you, with powerful new features. J. Comput. Chem. 39 (30) (2018)
Mark A. Hallen, Bruce Randall Donald
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. Bioinform. 33 (14) (2017)
Adegoke Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald
): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. RECOMB (2017)
Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. J. Comput. Biol. 24 (6) (2017)
Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald
A critical analysis of computational protein design with sparse residue interaction graphs. PLoS Comput. Biol. 13 (3) (2017)
Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency. RECOMB (2016)
Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J. Comput. Biol. 23 (6) (2016)
Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. J. Comput. Biol. 23 (9) (2016)
Mark A. Hallen, Bruce Randall Donald
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. J. Comput. Biol. 23 (5) (2016)
Seydou Traoré, Kyle E. Roberts, David Allouche, Bruce Randall Donald, Isabelle André, Thomas Schiex, Sophie Barbe
Fast search algorithms for computational protein design. J. Comput. Chem. 37 (12) (2016)
Mark Hallen, Bruce Randall Donald
Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. RECOMB (2015)
Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald
BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. RECOMB (2015)
Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng
An efficient parallel algorithm for accelerating computational protein design. Bioinform. 30 (12) (2014)
Bruce Randall Donald, Christopher G. Levey, Igor Paprotny, Daniela Rus
Planning and control for microassembly of structures composed of stress-engineered MEMS microrobots. Int. J. Robotics Res. 32 (2) (2013)
Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald
Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure. RECOMB (2013)
Himanshu Chandola, Bruce Randall Donald, Chris Bailey-Kellogg
Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data. BCB (2013)
Christopher G. Levey, Igor Paprotny, Bruce Randall Donald
MicroStressBots: Species Differentiation in Surface Micromachined Microrobots. SSR@ICRA (2013)
Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald
Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity. PLoS Comput. Biol. 8 (4) (2012)
Igor Paprotny, Christopher G. Levey, Paul Wright, Bruce Randall Donald
Turning-rate Selective Control : A New Method for Independent Control of Stress-engineered MEMS Microrobots. Robotics: Science and Systems (2012)
Bruce Randall Donald
The Compass That Steered Robotics. Logic and Program Semantics (2012)
Daniel A. Keedy, Ivelin Georgiev, Edward B. Triplett, Bruce Randall Donald, David C. Richardson, Jane S. Richardson
The Role of Local Backrub Motions in Evolved and Designed Mutations. PLoS Comput. Biol. 8 (8) (2012)
Pablo Gainza, Kyle E. Roberts, Bruce Randall Donald
Protein Design Using Continuous Rotamers. PLoS Comput. Biol. 8 (1) (2012)
Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. RECOMB (2011)
Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald
Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm. RECOMB (2011)
Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. RECOMB (2011)
Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald
Protein Loop Closure Using Orientational Restraints from NMR Data. RECOMB (2011)
Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs. J. Comput. Biol. 18 (11) (2011)
Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. J. Comput. Biol. 18 (11) (2011)
Mehmet Serkan Apaydin, Bülent Çatay, Nicholas Patrick, Bruce Randall Donald
NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments. Comput. J. 54 (5) (2011)
Himanshu Chandola, Anthony K. Yan, Shobha Potluri, Bruce Randall Donald, Chris Bailey-Kellogg
NMR Structural Inference of Symmetric Homo-Oligomers. J. Comput. Biol. 18 (12) (2011)
Mehmet Çagri Çalpur, Hakan Erdogan, Bülent Çatay, Bruce Randall Donald, Mehmet Serkan Apaydin
Developing a Scoring Function for NMR Structure-based Assignments using Machine Learning. ISCIS (2010)
Anna Yershova, Chittaranjan Tripathy, Pei Zhou, Bruce Randall Donald
Algorithms and Analytic Solutions Using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR. WAFR (2010)
Jianyang Zeng, Pei Zhou, Bruce Randall Donald
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. RECOMB (2010)
Mehmet Serkan Apaydin, Bülent Çatay, Nicholas Patrick, Bruce Randall Donald
NVR-BIP: Nuclear vector replacement using binary integer programming for NMR structure-based assignments. ISCIS (2009)
Bruce Randall Donald, Christopher G. Levey, Igor Paprotny, Daniela Rus
Simultaneous Control of Multiple MEMS Microrobots. WAFR (2008)
Ivelin Georgiev, Daniel A. Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald
Algorithm for backrub motions in protein design. ISMB (2008)
Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald
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. J. Comput. Chem. 29 (10) (2008)
Ivelin Georgiev, Bruce Randall Donald
Dead-End Elimination with Backbone Flexibility. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Shobha Potluri, Anthony K. Yan, James J. Chou, Bruce Randall Donald, Chris Bailey-Kellogg
Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints. WAFR (2006)
Lincong Wang, Ramgopal R. Mettu, Bruce Randall Donald
Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data. J. Comput. Biol. 13 (7) (2006)
Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. ISMB (Supplement of Bioinformatics) (2006)
Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald
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. RECOMB (2006)
Lincong Wang, Bruce Randall Donald
An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. CSB (2005)
Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald
High-throughput inference of protein-protein interfaces from unassigned NMR data. ISMB (Supplement of Bioinformatics) (2005)
Anthony K. Yan, Christopher James Langmead, Bruce Randall Donald
A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology. Int. J. Robotics Res. 24 (2-3) (2005)
Bruce Randall Donald, Christopher G. Levey, Craig D. McGray, Igor Paprotny, Daniela Rus
A Steerable, Untethered, 250 × 60µm MEMS Mobile Micro-Robot. ISRR (2005)
Bruce Randall Donald
Computational and physical modeling challenges in structural molecular biology and proteomics. Symposium on Solid and Physical Modeling (2005)
Lincong Wang, Ramgopal R. Mettu, Bruce Randall Donald
An Algebraic Geometry Approach to Protein Structure Determination from NMR Data. CSB (2005)
Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald
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. J. Comput. Biol. 12 (6) (2005)
Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald
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. RECOMB (2004)
Bruce Randall Donald
Algorithmic Challenges in Structural Molecular Biology and Proteomics. WAFR (2004)
Christopher James Langmead, Bruce Randall Donald
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment. CSB (2004)
Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald
A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. J. Comput. Biol. 11 (2/3) (2004)
Lincong Wang, Bruce Randall Donald
Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimum Number of Residual Dipolar Couplings. CSB (2004)
Ryan H. Lilien, Hany Farid, Bruce Randall Donald
Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum. J. Comput. Biol. 10 (6) (2003)
Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald
Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. RECOMB (2003)
Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald
Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns. J. Comput. Biol. 10 (3/4) (2003)
Bruce Randall Donald, Christopher G. Levey, Craig D. McGray, Daniela Rus, Mike Sinclair
UntetheredMicro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance. ISRR (2003)
Christopher James Langmead, Bruce Randall Donald
3D Structural Homology Detection via Unassigned Residual Dipolar Couplings. CSB (2003)
Lincong Wang, Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald
An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings. CSB (2003)
Bruce Randall Donald, Kevin M. Lynch, Daniela Rus
Guest Editors' Introduction to the Special Issue on Algorithmic Foundations of Robotics. Int. J. Robotics Res. 21 (3) (2002)
Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald
Phase-independent rhythmic analysis of genome-wide expression patterns. RECOMB (2002)
Christopher James Langmead, C. Robertson McClung, Bruce Randall Donald
A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns. CSB (2002)
Christopher James Langmead, Bruce Randall Donald
Extracting structural information using time-frequency analysis of protein NMR data. RECOMB (2001)
Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. J. Comput. Biol. 8 (1) (2001)
Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien
Physical Geometric Algorithms for Structural Molecular Biology. ICRA (2001)
Amy J. Briggs, Bruce Randall Donald
Visibility-Based Planning of Sensor Control Strategies. Algorithmica 26 (3-4) (2000)
Bruce Randall Donald, Frederick Henle
Using Haptic Vector Fields for Animation Motion Control. ICRA (2000)
Russell G. Brown, Bruce Randall Donald
Mobile Robot Self-Localization without Explicit Landmarks. Algorithmica 26 (3-4) (2000)
Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. ISMB (2000)
Karl-Friedrich Böhringer, Vivek Bhatt, Bruce Randall Donald, Kenneth Y. Goldberg
Algorithms for Sensorless Manipulation Using a Vibrating Surface. Algorithmica 26 (3-4) (2000)
Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. RECOMB (2000)
Karl-Friedrich Böhringer, Bruce Randall Donald, Lydia E. Kavraki, Florent Lamiraux
Part orientation with one or two stable equilibria using programmable force fields. IEEE Trans. Robotics Autom. 16 (2) (2000)
Tom Ngo, Doug Cutrell, Jenny Dana, Bruce Randall Donald, Lorie Loeb, Shunhui Zhu
Accessible animation and customizable graphics via simplicial configuration modeling. SIGGRAPH (2000)
Jon Howell, Bruce Randall Donald
Practical Mobile Robot Self-Localization. ICRA (2000)
John W. Suh, R. Bruce Darling, Karl-Friedrich Böhringer, Bruce Randall Donald, Henry Baltes, Gregory T. A. Kovacs
Fully Programmable MEMS Ciliary Actuator Arrays for Micromanipulation Tasks. ICRA (2000)
Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald
The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data. J. Comput. Biol. 7 (3-4) (2000)
Bruce Randall Donald, Larry Gariepy, Daniela Rus
Distributed Manipulation of Multiple Objects using Ropes. ICRA (2000)
Bruce Randall Donald, Larry Gariepy, Daniela Rus
Experiments in Constrained Prehensile Manipulation: Distributed Manipulation with Ropes. ISER (1999)
Karl-Friedrich Böhringer, Bruce Randall Donald, Noel C. MacDonald
Programmable Force Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders. Int. J. Robotics Res. 18 (2) (1999)
Karl-Friedrich Böhringer, Bruce Randall Donald, Dan Halperin
On the Area Bisectors of a Polygon. Discret. Comput. Geom. 22 (2) (1999)
Karl-Friedrich Böhringer, John W. Suh, Bruce Randall Donald, Gregory T. A. Kovacs
Vector fields for task-level distributed manipulation: experiments with organic micro actuator arrays. ICRA (1997)
Bruce Randall Donald, James S. Jennings, Daniela Rus
Information Invariants for Distributed Manipulation. Int. J. Robotics Res. 16 (5) (1997)
Bruce Randall Donald, James S. Jennings, Daniela Rus
Minimalism Distribution Supermodularity. J. Exp. Theor. Artif. Intell. 9 (2-3) (1997)
Karl-Friedrich Böhringer, Bruce Randall Donald, Dan Halperin
The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields. SCG (1997)
Karl-Friedrich Böhringer, Bruce Randall Donald, Noel C. MacDonald
What programmable vector fields can (and cannot) do: force field algorithms for MEMS and vibratory plate parts feeders. ICRA (1996)
Bruce Randall Donald, Patrick G. Xavier
Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open-Chain Manipulators. Algorithmica 14 (6) (1995)
Bruce Randall Donald, Patrick G. Xavier
Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds. Algorithmica 14 (6) (1995)
Daniela Rus, Bruce Randall Donald, Jim Jennings
Moving furniture with teams of autonomous robots. IROS (1) (1995)
Bruce Randall Donald
On Information Invariants in Robotics. Artif. Intell. 72 (1-2) (1995)

Bruce Randall Donald

Publication Activity (10 Years)

Top Topics

Top Venues