ArticleBioinformatics (Oxford, England)2017
SnapDock-template-based docking by Geometric Hashing.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Docking Foundations: From Rigid to Flexible Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- Pushing the accuracy limit of shape complementarity for protein-protein docking.BMC bioinformatics · 2019Article
- Identifying protein-protein interface via a novel multi-scale local sequence and structural representation.BMC bioinformatics · 2019Article
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs.Nucleic acids research · 2018Article
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Authors and funding
2 authors.
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Abstract
motivationA highly efficient template-based protein-protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein-protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well.
resultsTo evaluate the performance of the algorithm a blind re-modelling of 3547 PDB complexes, which have been uploaded after the PIFACE publication has been performed with success ratio of about 35%. Interestingly, a similar experiment with the template free PatchDock docking algorithm yielded a success rate of about 23% with roughly 1/3 of the solutions different from those of SnapDock. Consequently, the combination of the two methods gave a 42% success ratio. AVAILABILITY AND IMPLEMENTATION: A web server of the application is under development. CONTACT: michaelestrin@gmail.com or wolfson@tau.ac.il.
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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.