Rigid Body Energy Minimization on Manifolds for Molecular Docking.
Hanieh Mirzaei,Dmitri Beglov,Ioannis Ch. Paschalidis,Sandor Vajda,Pirooz Vakili,Dima Kozakov +5 more
Reads0
Chats0
TLDR
An efficient rigid-body optimization algorithm that, compared to the most widely used algorithms, converges approximately an order of magnitude faster to conformations with equal or slightly lower energy.Abstract:
Virtually all docking methods include some local continuous minimization of an energy/scoring function in order to remove steric clashes and obtain more reliable energy values. In this paper, we describe an efficient rigid-body optimization algorithm that, compared to the most widely used algorithms, converges approximately an order of magnitude faster to conformations with equal or slightly lower energy. The space of rigid body transformations is a nonlinear manifold, namely, a space which locally resembles a Euclidean space. We use a canonical parametrization of the manifold, called the exponential parametrization, to map the Euclidean tangent space of the manifold onto the manifold itself. Thus, we locally transform the rigid body optimization to an optimization over a Euclidean space where basic optimization algorithms are applicable. Compared to commonly used methods, this formulation substantially reduces the dimension of the search space. As a result, it requires far fewer costly function and gradi...read more
Citations
More filters
Journal ArticleDOI
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review.
TL;DR: This review discusses the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline.
Journal ArticleDOI
Modeling protein association mechanisms and kinetics.
Huan-Xiang Zhou,Paul A. Bates +1 more
TL;DR: Progress has been made in the modeling of protein association kinetics under conditions mimicking the heterogeneous, crowded environments of cells, an endeavor that should ultimately lead to a better understanding of cellular functions.
Journal ArticleDOI
Encounter complexes and dimensionality reduction in protein-protein association.
Dima Kozakov,Keyong Li,David R. Hall,Dmitri Beglov,Jiefu Zheng,Pirooz Vakili,Ora Schueler-Furman,Ioannis Ch. Paschalidis,G. Marius Clore,Sandor Vajda +9 more
TL;DR: Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion, similar to sliding of a protein along DNA in the process of protein-DNA recognition.
Journal ArticleDOI
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses.
TL;DR: A consistent scheme for pose scoring and gradient-based pose optimization of protein-ligand poses, consisting of a novel variant of the BFGS algorithm enabling step-length control, named LSL-BFGS (limited step length BFGS), and the empirical JAMDA scoring function designed for pose prediction and good numerical optimizability.
Journal ArticleDOI
Energy Minimization on Manifolds for Docking Flexible Molecules.
Hanieh Mirzaei,Shahrooz Zarbafian,Elizabeth A. Villar,Scott E. Mottarella,Dmitri Beglov,Sandor Vajda,Ioannis Ch. Paschalidis,Pirooz Vakili,Dima Kozakov +8 more
TL;DR: A recently introduced rigid body minimization algorithm, defined on manifolds, is extended to the problem of minimizing the energy of interacting flexible molecules and is general enough to be used in a large class of applications such as docking multidomain proteins with flexible hinges.
References
More filters
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
On the limited memory BFGS method for large scale optimization
Dong C. Liu,Jorge Nocedal +1 more
TL;DR: The numerical tests indicate that the L-BFGS method is faster than the method of Buckley and LeNir, and is better able to use additional storage to accelerate convergence, and the convergence properties are studied to prove global convergence on uniformly convex problems.
Book
A Mathematical Introduction to Robotic Manipulation
TL;DR: In this paper, the authors present a detailed overview of the history of multifingered hands and dextrous manipulation, and present a mathematical model for steerable and non-driveable hands.
Journal ArticleDOI
ZDOCK: An initial-stage protein-docking algorithm
Rong Chen,Li Li,Zhiping Weng +2 more
TL;DR: A new scoring function for the initial stage of unbound docking is presented that combines the recently developed pairwise shape complementarity with desolvation and electrostatics and shows superior performance, especially for the antibody‐antigen category of test cases.