Abstract
Autodock and its various variants are widely utilized docking approaches, which adopt optimization methods as search algorithms for flexible ligand docking and virtual screening. However, many of them have their limitations, such as poor accuracy for dockings with highly flexible ligands and low docking efficiency. In this paper, a multi-swarm optimization algorithm integrated with Autodock environment is proposed to design a high-performance and high-efficiency docking program, namely, MSLDOCK. The search algorithm is a combination of the random drift particle swarm optimization with a novel multi-swarm strategy and the Solis and Wets local search method with a modified implementation. Due to the algorithm's structure, MSLDOCK also has a multithread mode. The experimental results reveal that MSLDOCK outperforms other two Autodock-based approaches in many aspects, such as self-docking, cross-docking, and virtual screening accuracies as well as docking efficiency. Moreover, compared with three non-Autodock-based docking programs, MSLDOCK can be a reliable choice for self-docking and virtual screening, especially for dealing with highly flexible ligand docking problems. The source code of MSLDOCK can be downloaded for free from https://github.com/lcmeteor/MSLDOCK.
| Original language | English |
|---|---|
| Pages (from-to) | 1500-1515 |
| Number of pages | 16 |
| Journal | Journal of Chemical Information and Modeling |
| Volume | 61 |
| Issue number | 3 |
| Early online date | 4 Mar 2021 |
| DOIs | |
| Publication status | Published - 22 Mar 2021 |
Funder
Funding Information: This work was supported in part by the National Natural Science Foundation of China (projects numbers 61673194, 61672263, and 61672265) and in part by the National First-Class Discipline Program of Light Industry Technology and Engineering (project number LITE2018-25). Publisher Copyright: ©Keywords
- Library and Information Sciences
- Computer Science Applications
- General Chemical Engineering
- General Chemistry