Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites.

ABSTRACT: Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity co

SUBMITTER: Xiao W 

PROVIDER: S-EPMC6225211 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature