Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motif, Biomedical engineering online, 16:71, 2017 - the paper presents an example test case of the protocol for protein-protein docking in which CABS-dock is used for docking a short linear motif as a peptide. Highly flexible protein-peptide docking using CABS-dock, Methods in Molecular Biology, 1561: 69-94, 2017 - the paper presents an example of CABS-dock application for docking a potentially therapeutic peptide to a protein target, simulation contact maps (a new feature of the web server), tutorial for running CABS-dock web server from the command line or command line scripts Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction, Scientific Reports 6, 37532, 2016 - the paper presents CABS-dock application to simulations of the binding of the p53-MDM2 complex, including large-scale structural rearrangements of MDM2 flexible regions Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking, Methods, 93, 72-83, 2016 - the paper presents: example CABS-dock results obtained in the default mode and using advanced options that enable to increase the range of flexibility for chosen receptor fragments, examples of scoring of CABS-dock models using all-atom molecular dynamics, a tutorial appendix for analysis and visualization of CABS-dock results using VMD Papers describing the CABS-dock server and its example applications:ĬABS-dock web server for flexible docking of peptides to proteins without prior knowledge of the binding site, Nucleic Acids Research, 43(W1): W419-W424, 2015 - the paper describes CABS-dock web server implementation and results obtained for the PeptiDB benchmark set in the default mode (using peptide sequence, peptide secondary structure and receptor structure input informations) The plot has been made using a few months data from CABS-dock web server Plot below presents average simulation time (in hours) and min/max times for jobs in a function of a protein-peptide system size (receptor + protein) size, for default number of simulation cycles (50), using single 2.5 GHz processors. Note that CABSdock modeling scheme allows to apply/modify distance restraints between selected CA atoms or betweenĬABS design and applications have been recently described in the review:Ĭhemical Reviews, 116:7898–7936, 2016 1.4 Average simulation time In CABS, single amino acid is represented by 4 atoms (or pseudo-atoms): C-alpha ( CA), C-beta ( CB), center of the mass of Side-Chain group ( SC) and center of the peptide bond ( cp). The picture below showsĬomparison between all-atom representation (left) and CABS coarse-grained model representation (right) for an example 4-residue protein fragment.
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The movie below shows shows example simulation snapshots from the CABSdock study on molecular docking with large-scale conformational changes: the p53-MDM2 interaction, see details inĬABSdock method uses an efficient simulation engine: CABS coarse-grained protein model. The docking was performed with default CABSdock settings: (system replicas) and selected 1 trajectory together with RMSD analysis. The movie below shows example trajectories from protein-peptide docking using CABSdock. Out of 10 trajectories (system replicas) is presented. The movie below shows example trajectory from protein-peptide docking using CABSdock. The picture below shows the CABSdock pipeline with default settings. CABSdock standalone package allows for control and The method enables to simulate significantĬonformational changes during the docking search for a binding site. CABSflex simulations of protein fluctuationsĬABSdock is an efficient simulation method for protein-peptide docking. Output plots and additional analysis to reference complexĥ.3 Contact map and contact histogram plot analysisĥ.4 Handling of not identical input and reference modelsĦ.1 Analysis of an already finished simulationĩ.
Welcome to CABSdock wiki page! Installation instructions and the method outline are provided on theġ.5 Papers on CABSdock development and applicationsģ.2 Default docking, peptide sequence from PDBģ.5 Intrinsically unstructured protein regionsģ.9 Calculating ligand-RMSD values to a reference complexģ.10 Refinement of CABS-dock models using Rosetta FlexPepDockĥ.
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