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Journal of Molecular Biology|April 8, 2018
ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein DockingMikhail Ignatov, Andrey Kazennov, Dima KozakovMethods in Molecular Biology (Clifton, N.J.)|July 5, 2020
Protein-Protein and Protein-Peptide Docking with ClusPro ServerAndrey Alekseenko, Mikhail Ignatov, George Jones, et al.Journal of Computer-Aided Molecular Design|November 14, 2018
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand ChallengeMikhail Ignatov, Cong Liu, Andrey Alekseenko, et al.Journal of Molecular Biology|December 22, 2019
ClusPro LigTBM: Automated Template-based Small Molecule DockingAndrey Alekseenko, Sergei Kotelnikov, Mikhail Ignatov, et al.Frontiers in Bioinformatics|September 4, 2023
Improved prediction of MHC-peptide binding using protein language modelsNasser Hashemi, Boran Hao, Mikhail Ignatov, et al.Proceedings of the National Academy of Sciences of the United States of America|July 15, 2016
Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifoldsDzmitry Padhorny, Andrey Kazennov, Brandon S Zerbe, et al.Journal of Computer-Aided Molecular Design|December 28, 2019
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, et al.Current Opinion in Structural Biology|March 31, 2009
Convergence and combination of methods in protein-protein dockingSandor Vajda, Dima KozakovBioinformatics (Oxford, England)|July 1, 2016
Accounting for pairwise distance restraints in FFT-based protein-protein dockingBing Xia, Sandor Vajda, Dima KozakovPlos Computational Biology|October 3, 2014
Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfacesTanggis Bohnuud, Dima Kozakov, Sandor VajdaPageof 15