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A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility

Varela, Daniel LU orcid ; Karlin, Vera LU and André, Ingemar LU orcid (2022) In Structure 30(11). p.3-1558
Abstract

Protein complex formation is encoded by specific interactions at the atomic scale, but the computational cost of modeling proteins at this level often requires use of simplified energy models and limited conformational flexibility. In particular, use of all-atom energy functions and backbone and side-chain flexibility results in rugged energy landscapes that are difficult to explore. In this study, we develop a protein-protein docking algorithm, EvoDOCK, that combines the strength of a differential evolution algorithm for efficient exploration of the global search space with the benefits of a local optimization method to refine detailed atomic interactions. EvoDOCK enabled accurate and fast local and global protein-protein docking using... (More)

Protein complex formation is encoded by specific interactions at the atomic scale, but the computational cost of modeling proteins at this level often requires use of simplified energy models and limited conformational flexibility. In particular, use of all-atom energy functions and backbone and side-chain flexibility results in rugged energy landscapes that are difficult to explore. In this study, we develop a protein-protein docking algorithm, EvoDOCK, that combines the strength of a differential evolution algorithm for efficient exploration of the global search space with the benefits of a local optimization method to refine detailed atomic interactions. EvoDOCK enabled accurate and fast local and global protein-protein docking using an all-atom energy function with side-chain flexibility. Comparison with a standard method built on Monte Carlo optimization demonstrated improved accuracy and increases in computational speed of up to 35 times. The evolutionary algorithm also enabled efficient atomistic docking with backbone flexibility.

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Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
backbone flexibility, global docking, memetic algorithm, protein docking, protein-protein complexes, side-chain flexibility
in
Structure
volume
30
issue
11
pages
3 - 1558
publisher
Cell Press
external identifiers
  • pmid:36265485
  • scopus:85140953336
ISSN
0969-2126
DOI
10.1016/j.str.2022.09.005
language
English
LU publication?
yes
id
8e7bfed7-e1d4-41d1-a481-ab9494da9126
date added to LUP
2022-11-30 08:37:15
date last changed
2024-04-16 12:37:34
@article{8e7bfed7-e1d4-41d1-a481-ab9494da9126,
  abstract     = {{<p>Protein complex formation is encoded by specific interactions at the atomic scale, but the computational cost of modeling proteins at this level often requires use of simplified energy models and limited conformational flexibility. In particular, use of all-atom energy functions and backbone and side-chain flexibility results in rugged energy landscapes that are difficult to explore. In this study, we develop a protein-protein docking algorithm, EvoDOCK, that combines the strength of a differential evolution algorithm for efficient exploration of the global search space with the benefits of a local optimization method to refine detailed atomic interactions. EvoDOCK enabled accurate and fast local and global protein-protein docking using an all-atom energy function with side-chain flexibility. Comparison with a standard method built on Monte Carlo optimization demonstrated improved accuracy and increases in computational speed of up to 35 times. The evolutionary algorithm also enabled efficient atomistic docking with backbone flexibility.</p>}},
  author       = {{Varela, Daniel and Karlin, Vera and André, Ingemar}},
  issn         = {{0969-2126}},
  keywords     = {{backbone flexibility; global docking; memetic algorithm; protein docking; protein-protein complexes; side-chain flexibility}},
  language     = {{eng}},
  month        = {{11}},
  number       = {{11}},
  pages        = {{3--1558}},
  publisher    = {{Cell Press}},
  series       = {{Structure}},
  title        = {{A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility}},
  url          = {{http://dx.doi.org/10.1016/j.str.2022.09.005}},
  doi          = {{10.1016/j.str.2022.09.005}},
  volume       = {{30}},
  year         = {{2022}},
}