ArticleJournal of chemical information and modeling2014
Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Expanding the Palette of Molecular Fragments for Small Molecule De Novo Design Through Isosteric Swapping.Journal of computational chemistry · 2026Article
- Hands-On Docking with Molegro Virtual Docker.Methods in molecular biology (Clifton, N.J.) · 2026Article
- OTMol: Robust Molecular Structure Comparison via Optimal Transport.Journal of chemical information and modeling · 2025Article
- Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.Journal of chemical information and modeling · 2025Article
- Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK.Journal of computational chemistry · 2025Article
- Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Continuous symmetry and chirality measures: approximate algorithms for large molecular structures.Journal of cheminformatics · 2023Article
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- Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.Protein science : a publication of the Protein Society · 2023Article
- Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A molecular evolution algorithm for ligand design in DOCK.Journal of computational chemistry · 2022Article
- Structure-based discovery of nonopioid analgesics acting through the αScience (New York, N.Y.) · 2022Article
- Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2.bioRxiv : the preprint server for biology · 2022Article
- Protein-Ligand Docking in the Machine-Learning Era.Molecules (Basel, Switzerland) · 2022Review
- Identifying molecular structural features by pattern recognition methods.RSC advances · 2022Article
- Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.Journal of molecular biology · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
False negative docking outcomes for highly symmetric molecules are a barrier to the accurate evaluation of docking programs, scoring functions, and protocols. This work describes an implementation of a symmetry-corrected root-mean-square deviation (RMSD) method into the program DOCK based on the Hungarian algorithm for solving the minimum assignment problem, which dynamically assigns atom correspondence in molecules with symmetry. The algorithm adds only a trivial amount of computation time to the RMSD calculations and is shown to increase the reported overall docking success rate by approximately 5% when tested over 1043 receptor-ligand systems. For some families of protein systems the results are even more dramatic, with success rate increases up to 16.7%. Several additional applications of the method are also presented including as a pairwise similarity metric to compare molecules during de novo design, as a scoring function to rank-order virtual screening results, and for the analysis of trajectories from molecular dynamics simulation. The new method, including source code, is available to registered users of DOCK6 ( http://dock.compbio.ucsf.edu ).
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