AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

ABSTRACT: AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive

SUBMITTER: Labbe CM 

PROVIDER: S-EPMC5570140 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature