Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin.

ABSTRACT: Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket and contribute to the free energy of binding. It would thus be extremely useful to be able to accurately predict the position and orientation of water molecules within a binding pocket. Recently, we developed the WaterDock protocol that was able to predict 97% of the water molecules in a test set. However, this approach generated false positives at a rate of over 20% in most cases and whilst this might be acceptable for some applications, in high throughput scenarios this is not desirable. Here we tackle this problem via the inclusion of knowledge regarding the solvation structure of ligand functional groups. We call this new protocol

SUBMITTER: Sridhar A 

PROVIDER: S-EPMC5325533 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature