AMMOS Software: Method and Application

Abstract

Recent advances in computational sciences enabled extensive use of in silico methods in projects at the interface between chemistry and biology. Among them virtual ligand screening, a modern set of approaches, facilitates hit identification and lead optimization in drug discovery programs. Most of these approaches require the preparation of the libraries containing small organic molecules to be screened or a refinement of the virtual screening results. Here we present an overview of the open source AMMOS software, which is a platform performing an automatic procedure that allows for a structural generation and optimization of drug-like molecules in compound collections, as well as a structural refinement of protein-ligand complexes to assist in silico screening exercises.

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

“…Following on the earlier work of Verdonk et al, where the reasons of docking failures were compared for fragments and small molecules, [105] Vass et al used Glide to further investigate factors affecting success rates for the placement of linked fragments in sequential fragment docking. [82,110] Using 129 protein-ligand complexes, they tested three sampling protocols [124] AMMOS www.mti.univ-paris-diderot.fr/en/downloads.html [216] AutoMap ligmap.sourceforge.net [142] Cell-Dock mmb.pcb.ub.es/~cpons/Cell-Dock [217] CovalentDock code.google.com/p/covalentdock [102] CRDOCK ub.cbm.uam.es [101] cudock code.google.com/p/cudock [218] DecoyFinder URVnutrigenomica-CTNS.github.com/DecoyFinder [219] DockoMatic sourceforge.net/projects/dockomatic [103] Dolina by request [13] eSimDock www.brylinski.org/esimdock [64] GalaxyDock galaxy.seoklab.org/softwares/galaxydock.html [4,5] FIPSDock by request [104] Fleksy www.cmbi.ru.nl/software/fleksy [21] MMPBSA.py ambermd.org [220] RDKit www.rdkit.org [221] RosettaLigand www.rosettacommons.org/software/ [7,144] S4MPLE infochim.u-strasbg.fr [50] VinaMPI cmb.ornl.gov/~sek/ [222] WaterDock sbcb.bioch.ox.ac.uk/waterdock [81] Servers, platforms, and web interfaces BSP-SLIM zhanglab.ccmb.med.umich.edu/BSP-SLIM [212] ChemBioServer bioserver-3.bioacademy.gr/Bioserver/ChemBioServer [223] CovalentDock Cloud docking.sce.ntu.edu.sg [224] FORECASTER fitted.ca [175] FTMap ftmap.bu.edu [225,226] FTSite ftsite.bu.edu [227] idTarget idtarget.rcas.sinica.edu.tw [228] pyDockWEB life.bsc.es/servlet/pydock [229] Robetta robe...…”

<em>In Silico</em> Screening and Analysis of Potential Inhibitors of Arylamine N-Acetyltransferases (NATs) from the Traditional Chinese Medicine: A Study Using Free Available Tools

“…This procedure was followed by the addition of hydrogens and attribution of the 3D structure for each compound with the Standardizer[47] software. Geometries of the ligands were then optimized with the AMMOS [48] software implemented in the Mobyle portal. Afterwards, the library was submitted to the FAF-Drugs3 [5,6] server.…”