Related Experiment Video
Updated: Nov 15, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
MSLDOCK: Multi-Swarm Optimization for Flexible Ligand Docking and Virtual Screening
Chao Li1, Jun Sun1, Vasile Palade2
1Department of Computer Science and Technology, Jiangnan University, No.1800, Lihu Avenue, Wuxi, Jiangsu 214122, PR China.
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.
More Related Videos
10:29Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
10:21Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
Published on: February 23, 2024
Related Concept Videos
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites
Ligand Binding and Linkage
Ligand Binding and Linkage
The Equilibrium Binding Constant and Binding Strength
Cooperative Allosteric Transitions