ArticleBMC bioinformatics2019
Pushing the accuracy limit of shape complementarity for protein-protein docking.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of NaScientific reports · 2024Article
- Advancements in small molecule drug design: A structural perspective.Drug discovery today · 2023Review
- EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations.Journal of molecular modeling · 2023Article
- General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model.Molecular biology and evolution · 2022Article
- HDOCK update for modeling protein-RNA/DNA complex structures.Protein science : a publication of the Protein Society · 2022Article
- SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro.International journal of molecular sciences · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease MPharmaceuticals (Basel, Switzerland) · 2022Article
- Improving peptide-protein docking with AlphaFold-Multimer using forced sampling.Frontiers in bioinformatics · 2022Article
- Shape Complementarity Optimization of Antibody-Antigen Interfaces: The Application to SARS-CoV-2 Spike Protein.Frontiers in molecular biosciences · 2022Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Plausible blockers of Spike RBD in SARS-CoV2-molecular design and underlying interaction dynamics from high-level structural descriptors.Journal of molecular modeling · 2021Article
- InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network.Frontiers in bioinformatics · 2021Review
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions.Journal of cheminformatics · 2020Review
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Article
- Docking-based identification of small-molecule binding sites at protein-protein interfaces.Computational and structural biotechnology journal · 2020Article
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2 authors.
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Abstract
backgroundProtein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open question in the development of protein-protein docking algorithms, especially for grid-based docking approaches.
resultsWe have proposed a new pairwise shape-based scoring function (LSC) for protein-protein docking which adopts an exponential form to take into account long-range interactions between protein atoms. The LSC scoring function was incorporated into our FFT-based docking program and evaluated for both bound and unbound docking on the protein docking benchmark 4.0. It was shown that our LSC achieved a significantly better performance than four other similar docking methods, ZDOCK 2.1, MolFit/G, GRAMM, and FTDock/G, in both success rate and number of hits. When considering the top 10 predictions, LSC obtained a success rate of 51.71% and 6.82% for bound and unbound docking, respectively, compared to 42.61% and 4.55% for the second-best program ZDOCK 2.1. LSC also yielded an average of 8.38 and 3.94 hits per complex in the top 1000 predictions for bound and unbound docking, respectively, followed by 6.38 and 2.96 hits for the second-best ZDOCK 2.1.
conclusionsThe present LSC method will not only provide an initial-stage docking approach for post-docking processes but also have a general implementation for accurate representation of other energy terms on grids in protein-protein docking. The software has been implemented in our HDOCK web server at http://hdock.phys.hust.edu.cn/.
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