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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  
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  ...  Chimera required about 10 minutes for 1 ligand and full protein flexibility minimization for a protein of typical length (350 residues).  ...  protein minimization (Case 1) with AMMOS2 (shown in cyan).  ... 
doi:10.1093/nar/gkx397 pmid:28486703 pmcid:PMC5570140 fatcat:nbxppa2yjvhu5nl7lnbcfrt5c4

A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

Nathalie Lagarde, Elodie Goldwaser, Tania Pencheva, Dessislava Jereva, Ilza Pajeva, Julien Rey, Pierre Tuffery, Bruno O. Villoutreix, Maria A. Miteva
2019 International Journal of Molecular Sciences  
(via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]).  ...  Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening  ...  /services/MTiOpenScreen/), and molecular mechanics optimization to refine the docked complexes via the web server AMMOS2 (Automatic Molecular Mechanics Optimization for in silico Screening) [21] (http  ... 
doi:10.3390/ijms20184648 pmid:31546814 pmcid:PMC6769597 fatcat:az52xjmesvc6tgsx4un2vzmhiu

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

2020 Briefings in Bioinformatics  
This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule  ...  different hypotheses in a timely fashion while contributing to teaching in the field of drug development.  ...  Dock/undock or rescoring tools Automatic Molecular Mechanics Optimization for in silico Screening (AMMOS2) is a web server for protein-ligand-water complexes refinement via molecular mechanics [255] .  ... 
doi:10.1093/bib/bbaa034 pmid:32187356 pmcid:PMC7986591 fatcat:mq3csvzjkfekhpjfti2wmyipxi

New machine learning and physics-based scoring functions for drug discovery

Isabella A. Guedes, André M. S. Barreto, Diogo Marinho, Eduardo Krempser, Mélaine A. Kuenemann, Olivier Sperandio, Laurent E. Dardenne, Maria A. Miteva
2021 Scientific Reports  
in silico drug design for diverse proteins as well as for specific targets such as proteases and proteinprotein interactions.  ...  ligand torsional entropy contribution to ligand binding.  ...  We have previously developed the AMMOS2 web server 82 , which permits to take into consideration the presence of explicit water molecules in the binding pocket in order to optimize the predicted protein-ligand  ... 
doi:10.1038/s41598-021-82410-1 pmid:33542326 pmcid:PMC7862620 fatcat:jstufcgu7ze4pndbtxdcenqvbq