Bruce Randall Donald
Orcid: 0000-0001-6884-4398Affiliations:
- Duke University, Durham, USA
According to our database1,
Bruce Randall Donald
authored at least 124 papers
between 1985 and 2022.
Collaborative distances:
Collaborative distances:
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Online presence:
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on zbmath.org
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on orcid.org
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on id.loc.gov
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on cs.duke.edu
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on dl.acm.org
On csauthors.net:
Bibliography
2022
PLoS Comput. Biol., 2022
J. Comput. Biol., 2022
Resistor: An Algorithm for Predicting Resistance Mutations Using Pareto Optimization over Multistate Protein Design and Mutational Signatures.
Proceedings of the Research in Computational Molecular Biology, 2022
2020
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., 2020
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape.
J. Comput. Biol., 2020
2019
Discret. Appl. Math., 2019
Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape.
Proceedings of the Research in Computational Molecular Biology, 2019
Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk).
Proceedings of the 35th International Symposium on Computational Geometry, 2019
2018
J. Comput. Chem., 2018
<i>BBK* (Branch and Bound Over K*): </i> A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces.
J. Comput. Biol., 2018
2017
A critical analysis of computational protein design with sparse residue interaction graphs.
PLoS Comput. Biol., 2017
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.
J. Comput. Biol., 2017
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.
Bioinform., 2017
BBK<sup>*</sup> (Branch and Bound over K<sup>*</sup>): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces.
Proceedings of the Research in Computational Molecular Biology, 2017
2016
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.
J. Comput. Biol., 2016
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design.
J. Comput. Biol., 2016
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., 2016
2015
Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.
Proceedings of the Research in Computational Molecular Biology, 2015
2014
Bioinform., 2014
2013
Planning and control for microassembly of structures composed of stress-engineered MEMS microrobots.
Int. J. Robotics Res., 2013
Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure.
Proceedings of the Research in Computational Molecular Biology, 2013
Proceedings of the Small-Scale Robotics. From Nano-to-Millimeter-Sized Robotic Systems and Applications, 2013
Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data.
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
PLoS Comput. Biol., 2012
PLoS Comput. Biol., 2012
Turning-rate Selective Control : A New Method for Independent Control of Stress-engineered MEMS Microrobots.
Proceedings of the Robotics: Science and Systems VIII, 2012
Proceedings of the Logic and Program Semantics, 2012
2011
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data.
J. Comput. Biol., 2011
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs.
J. Comput. Biol., 2011
NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.
Comput. J., 2011
Proceedings of the Research in Computational Molecular Biology, 2011
Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm.
Proceedings of the Research in Computational Molecular Biology, 2011
2010
Algorithms and Analytic Solutions Using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR.
Proceedings of the Algorithmic Foundations of Robotics IX, 2010
Proceedings of the Research in Computational Molecular Biology, 2010
Developing a Scoring Function for NMR Structure-based Assignments using Machine Learning.
Proceedings of the Computer and Information Sciences, 2010
2008
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., 2008
Proceedings of the Algorithmic Foundation of Robotics VIII, 2008
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008
2007
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
2006
A Polynomial-Time Algorithm for <i>De Novo</i> Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data.
J. Comput. Biol., 2006
Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints.
Proceedings of the Algorithmic Foundation of Robotics VII, 2006
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.
Proceedings of the Research in Computational Molecular Biology, 2006
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
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.
J. Comput. Biol., 2005
A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology.
Int. J. Robotics Res., 2005
Computational and physical modeling challenges in structural molecular biology and proteomics.
Proceedings of the Tenth ACM Symposium on Solid and Physical Modeling 2005, 2005
Proceedings of the Robotics Research: Results of the 12th International Symposium, 2005
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
2004
A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments.
J. Comput. Biol., 2004
Proceedings of the Algorithmic Foundations of Robotics VI, 2004
Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimum Number of Residual Dipolar Couplings.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2003
Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum.
J. Comput. Biol., 2003
J. Comput. Biol., 2003
Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003
UntetheredMicro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance.
Proceedings of the Robotics Research, The Eleventh International Symposium, 2003
An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
2002
Guest Editors' Introduction to the Special Issue on Algorithmic Foundations of Robotics.
Int. J. Robotics Res., 2002
A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002
2001
J. Comput. Biol., 2001
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001
Proceedings of the 2001 IEEE International Conference on Robotics and Automation, 2001
2000
IEEE Trans. Robotics Autom., 2000
The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data.
J. Comput. Biol., 2000
Accessible animation and customizable graphics via simplicial configuration modeling.
Proceedings of the 27th Annual Conference on Computer Graphics and Interactive Techniques, 2000
Proceedings of the 2000 IEEE International Conference on Robotics and Automation, 2000
Proceedings of the 2000 IEEE International Conference on Robotics and Automation, 2000
Proceedings of the 2000 IEEE International Conference on Robotics and Automation, 2000
Proceedings of the 2000 IEEE International Conference on Robotics and Automation, 2000
1999
Programmable Force Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders.
Int. J. Robotics Res., 1999
Experiments in Constrained Prehensile Manipulation: Distributed Manipulation with Ropes.
Proceedings of the Experimental Robotics VI, 1999
1997
Vector fields for task-level distributed manipulation: experiments with organic micro actuator arrays.
Proceedings of the 1997 IEEE International Conference on Robotics and Automation, 1997
Proceedings of the Thirteenth Annual Symposium on Computational Geometry, 1997
1996
What programmable vector fields can (and cannot) do: force field algorithms for MEMS and vibratory plate parts feeders.
Proceedings of the 1996 IEEE International Conference on Robotics and Automation, 1996
1995
Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open-Chain Manipulators.
Algorithmica, 1995
Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds.
Algorithmica, 1995
Proceedings of the Experimental Robotics IV, The 4th International Symposium, Stanford, California, USA, June 30, 1995
Proceedings of IEEE/RSJ International Conference on Intelligent Robots and Systems, 1995
1994
Proceedings of the 1994 International Conference on Robotics and Automation, 1994
Proceedings of the 1994 International Conference on Robotics and Automation, 1994
Proceedings of the 1994 International Conference on Robotics and Automation, 1994
1993
The Motion of Planar, Compliantly Connected Rigid Bodies in Contact, With Applications to Automatic Fastening.
Int. J. Robotics Res., 1993
Special Issue on Computational Robotics: The Geometric Theory of Manipulation, Planning, and Control.
Algorithmica, 1993
Proceedings of the 1993 IEEE International Conference on Robotics and Automation, 1993
Proceedings of the 1993 IEEE International Conference on Robotics and Automation, 1993
1992
Robotics Auton. Syst., 1992
Proceedings of the 1992 IEEE International Conference on Robotics and Automation, 1992
Proceedings of the 1992 IEEE International Conference on Robotics and Automation, 1992
Proceedings of the Eighth Annual Symposium on Computational Geometry, 1992
1991
Perceptual limits, perceptual equivalence classes, and a robot's sensori-computational capabilities (extended abstract).
Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems, 1991
Proceedings of the 1991 IEEE International Conference on Robotics and Automation, 1991
Sensor interpretation and task-directed planning using perceptual equivalence classes.
Proceedings of the 1991 IEEE International Conference on Robotics and Automation, 1991
Proceedings of the 32nd Annual Symposium on Foundations of Computer Science, 1991
1990
Int. J. Robotics Res., 1990
Algorithmica, 1990
Proceedings of the 17th Annual Conference on Computer Graphics and Interactive Techniques, 1990
On the motion of compliantly-connected rigid bodies in contact. II. A system for analyzing designs for assembly.
Proceedings of the 1990 IEEE International Conference on Robotics and Automation, 1990
1989
Towards experimental verification of an automated compliant motion planner based on a geometric theory of error detection and recovery.
Proceedings of the 1989 IEEE International Conference on Robotics and Automation, 1989
Proceedings of the 1989 IEEE International Conference on Robotics and Automation, 1989
Lecture Notes in Computer Science 336, Springer, ISBN: 3-540-96909-8, 1989
1988
A Geometric Approach to Error Detection and Recovery for Robot Motion Planning with Uncertainty.
Artif. Intell., 1988
Proceedings of the 1988 IEEE International Conference on Robotics and Automation, 1988
Proceedings of the 29th Annual Symposium on Foundations of Computer Science, 1988
1987
Artif. Intell., 1987
1986
Robot motion planning with uncertainty in the geometric models of the robot and environment: A formal framework for error detection and recovery.
Proceedings of the 1986 IEEE International Conference on Robotics and Automation, 1986
1985
On motion planning with six degrees of freedom: Solving the intersection problems in configuration space.
Proceedings of the 1985 IEEE International Conference on Robotics and Automation, 1985