DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
Copyright policy )DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
AbstractMotivationRecent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).ResultsEnsembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.Availabilitydinc-covid.kavrakilab.orgSupplementary informationDetails on methods for ensemble generation and docking are provided as supplementary data online.Contactgeancarlo.zanatta@ufc.br,kavraki@rice.edu
- University of Strathclyde United Kingdom
- Universidade Federal do Ceará Brazil
- University of Grenoble France
- University of Houston United States
- RICE UNIVERSITY
FOS: Computer and information sciences, Medicine (General), Computational chemistry, Infectious disease (medical specialty), FOS: Health sciences, Biochemistry, Gene, Computational biology, Pathology, Disease, Heterocyclic Compounds for Drug Discovery, Drug discovery, Statistics, Molecular Docking, World Wide Web, Chemistry, Infectious Diseases, Computational Theory and Mathematics, Physical Sciences, Medicine, The Internet, Computational Methods in Drug Discovery, Receptor, Virtual screening, 570, Binding affinities, Bioinformatics, Flexibility (engineering), Docking (animal), Nursing, Coronavirus Disease 2019 Research, Molecular dynamics, Article, Binding site, FOS: Chemical sciences, Protein Data Bank, Virology, Web server, Health Sciences, FOS: Mathematics, Biology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Organic Chemistry, In silico, 540, Computer science, Coronavirus disease 2019 (COVID-19), Structural bioinformatics, Electronic computers. Computer science, Computer Science, Protein structure, Mathematics
FOS: Computer and information sciences, Medicine (General), Computational chemistry, Infectious disease (medical specialty), FOS: Health sciences, Biochemistry, Gene, Computational biology, Pathology, Disease, Heterocyclic Compounds for Drug Discovery, Drug discovery, Statistics, Molecular Docking, World Wide Web, Chemistry, Infectious Diseases, Computational Theory and Mathematics, Physical Sciences, Medicine, The Internet, Computational Methods in Drug Discovery, Receptor, Virtual screening, 570, Binding affinities, Bioinformatics, Flexibility (engineering), Docking (animal), Nursing, Coronavirus Disease 2019 Research, Molecular dynamics, Article, Binding site, FOS: Chemical sciences, Protein Data Bank, Virology, Web server, Health Sciences, FOS: Mathematics, Biology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Organic Chemistry, In silico, 540, Computer science, Coronavirus disease 2019 (COVID-19), Structural bioinformatics, Electronic computers. Computer science, Computer Science, Protein structure, Mathematics
selected citations These citations are derived from selected sources.This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).12 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Top 10% influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Average impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Top 10%
Citations provided by BIP!Popularity provided by BIP!