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CC-BY - Uznanie autorstwaProtein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
| cris.lastimport.scopus | 2024-02-12T19:33:57Z |
| dc.abstract.en | 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. |
| dc.affiliation | Uniwersytet Warszawski |
| dc.contributor.author | Kmiecik, Sebastian |
| dc.contributor.author | Koliński, Andrzej |
| dc.contributor.author | Kurciński, Mateusz |
| dc.contributor.author | Zalewski, Mateusz |
| dc.date.accessioned | 2024-01-25T18:20:48Z |
| dc.date.available | 2024-01-25T18:20:48Z |
| dc.date.copyright | 2021-07-08 |
| dc.date.issued | 2021 |
| dc.description.accesstime | AT_PUBLICATION |
| dc.description.finance | Publikacja bezkosztowa |
| dc.description.number | 14 |
| dc.description.version | FINAL_PUBLISHED |
| dc.description.volume | 22 |
| dc.identifier.doi | 10.3390/IJMS22147341 |
| dc.identifier.issn | 1422-0067 |
| dc.identifier.uri | https://repozytorium.uw.edu.pl//handle/item/117301 |
| dc.identifier.weblink | https://www.mdpi.com/1422-0067/22/14/7341/pdf |
| dc.language | eng |
| dc.pbn.affiliation | chemical sciences |
| dc.relation.ispartof | International Journal of Molecular Sciences |
| dc.relation.pages | 7341 |
| dc.rights | CC-BY |
| dc.sciencecloud | nosend |
| dc.subject.en | protein–protein interactions |
| dc.subject.en | protein–protein binding |
| dc.subject.en | protein–protein complex |
| dc.subject.en | coarsegrained modeling |
| dc.subject.en | multiscale modeling |
| dc.title | Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations |
| dc.type | JournalArticle |
| dspace.entity.type | Publication |