Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.
Int J Mol Sci
; 22(14)2021 Jul 08.
Article
em En
| MEDLINE
| ID: mdl-34298961
ABSTRACT
Most of the protein-protein docking methods treat proteins as almost rigid objects. Only the side-chains flexibility is usually taken into account. The few approaches enabling docking with a flexible backbone typically work in two steps, in which the search for protein-protein orientations and structure flexibility are simulated separately. In this work, we propose a new straightforward approach for docking sampling. It consists of a single simulation step during which a protein undergoes large-scale backbone rearrangements, rotations, and translations. Simultaneously, the other protein exhibits small backbone fluctuations. Such extensive sampling was possible using the CABS coarse-grained protein model and Replica Exchange Monte Carlo dynamics at a reasonable computational cost. In our proof-of-concept simulations of 62 protein-protein complexes, we obtained acceptable quality models for a significant number of cases.
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Base de dados:
MEDLINE
Assunto principal:
Proteínas
/
Dobramento de Proteína
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Simulação de Dinâmica Molecular
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Simulação de Acoplamento Molecular
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article