A Novel Algorithm to Predict Bridging Water Locations During Computational Ligand Docking

Access full-text files

Date

2019

Authors

Shub, Laura

Journal Title

Journal ISSN

Volume Title

Publisher

Abstract

Water molecules at the protein-ligand interface often form hydrogen bonds with both the ligand and the protein, affecting the structure and specificity of the association. These ‘bridging waters’ are typically omitted during ligand docking simulations due to the increased computational complexity they introduce. However, their inclusion has been shown to improve the accuracy of predicted docked structures. This is especially significant due to the use of these structures in computer-aided drug design. In this study, we demonstrate the performance of a new, efficient algorithm to predict the location of bridging waters and incorporate them into the final predicted structure of the protein-ligand complex on a small benchmark set of associations. Our results suggest that a rough, structure-based approach could be a valid method to both quickly and accurately predict the location of bridging waters, improving our ability to computationally screen drug candidates.

Department

Description

LCSH Subject Headings

Citation

Collections