UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
| Autor: | Agnieszka S. Karczyńska, Cezary Czaplewski, Adam Liwo, Paweł Krupa, Magdalena A. Mozolewska |
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| Rok vydání: | 2020 |
| Předmět: |
Statistics and Probability
Protein Conformation Computer science 030303 biophysics Peptide Computational biology Molecular Dynamics Simulation Biochemistry Molecular Docking Simulation 03 medical and health sciences Molecular dynamics Protein structure DOCK Macromolecular docking Molecular Biology 030304 developmental biology chemistry.chemical_classification 0303 health sciences Replica Proteins Computer Science Applications Computational Mathematics Computational Theory and Mathematics chemistry Docking (molecular) Peptides |
| Zdroj: | Bioinformatics. 37:1613-1615 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide–protein and protein–protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. Results We present a new protein–protein and peptide–protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide–protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. Availability and implementation UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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