AMMOS Software: Method and Application

  • T. Pencheva
  • D. Lagorce
  • I. Pajeva
  • B. O. Villoutreix
  • M. A. Miteva
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 819)

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.

Key words

3D structure generation Structure refinement Virtual screening AMMOS AMMP Open source/free software 

Notes

Acknowledgement

We thank the financial supports from the INSERM and University Paris Diderot. TP, MM and IP acknowledge the support of the Bulgarian National Science Fund (grants No. DTK02/58 and No. DO02/52).

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • T. Pencheva
    • 1
  • D. Lagorce
    • 2
  • I. Pajeva
    • 1
  • B. O. Villoutreix
    • 2
  • M. A. Miteva
    • 2
  1. 1.Institute of Biophysics and Biomedical EngineeringBulgarian Academy of SciencesSofiaBulgaria
  2. 2.Molécules Thérapeutiques in SilicoUniversité Paris DiderotParisFrance

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