ArticleJournal of chemical theory and computation2012
Rigid Body Energy Minimization on Manifolds for Molecular Docking.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Molecular docking and dynamics simulation studies uncover the host-pathogen protein-protein interactions in soybean (Frontiers in bioinformatics · 2026Article
- Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism.Molecules (Basel, Switzerland) · 2024Article
- Improved cluster ranking in protein-protein docking using a regression approach.Computational and structural biotechnology journal · 2021Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.Journal of computer-aided molecular design · 2019Article
- Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes.Scientific reports · 2018Article
- DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles.BMC structural biology · 2017Article
- Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.BMC bioinformatics · 2015Article
- The impact of side-chain packing on protein docking refinement.Journal of chemical information and modeling · 2015Article
- Energy Minimization on Manifolds for Docking Flexible Molecules.Journal of chemical theory and computation · 2015Article
- A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2014Article
- Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2014Article
- Article
- Modeling protein association mechanisms and kinetics.Current opinion in structural biology · 2013Review
- A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein DockingProceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2013Article
- Flexible Refinement of Protein-Ligand Docking on Manifolds.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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 gradient evaluations and leads to a more efficient algorithm. We have selected the LBFGS quasi-Newton method for local optimization since it uses only gradient information to obtain second order information about the energy function and avoids the far more costly direct Hessian evaluations. Two applications, one in protein-protein docking, and the other in protein-small molecular interactions, as part of macromolecular docking protocols are presented. The code is available to the community under open source license, and with minimal effort can be incorporated into any molecular modeling package.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.