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

Céline M. Labbé, Tania Pencheva, Dessislava Jereva, Dimitri Desvillechabrol, Jérôme Becot, Bruno O. Villoutreix, Ilza Pajeva, Maria A. Miteva
2017 Nucleic Acids Research  
Figure 1S . Protein-ligand interaction energies (in kcal/mol) before and after minimization with AMMOS2 for the best docking pose with different number of water molecules in the binding pocket for thrombin, HIV-1 protease, estrogen receptor, ribonuclease, carboxypeptidase, metalloproteinase. C0 notes the energy of the docked complex before minimization, C1 to C5 correspond to the five cases of protein flexibility. The PDB ID of the proteins are noted. Figure 2S . Protein-ligand interaction
more » ... ies (in kcal/mol) calculated with the AMMOS2 server after docking with AutoDock4.2 (in blue), after minimization with Chimera (in orange) and after minimization with AMMOS2 (in grey) including all water molecules present in the X-ray structures within a distance of 6 Å of the co-crystallized ligand. A. Protein flexibility Case 1; B. Protein flexibility Case 3. Chimera minimization included 1000 steps of steepest descent optimization and water molecules and metal ions were considered as a part of the receptor. Chimera required about 10 minutes for 1 ligand and full protein flexibility minimization for a protein of typical length (350 residues).
doi:10.1093/nar/gkx397 pmid:28486703 pmcid:PMC5570140 fatcat:nbxppa2yjvhu5nl7lnbcfrt5c4