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Nucleic Acids Research Advance Access originally published online on October 25, 2007
Nucleic Acids Research 2008 36(Database issue):D360-D367; doi:10.1093/nar/gkm887
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Nucleic Acids Research, 2008, Vol. 36, Database issue D360-D367
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-com

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

François-Yves Dupradeau1,*, Christine Cézard1, Rodolphe Lelong1, Élodie Stanislawiak1, Julien Pêcher1, Jean Charles Delepine2 and Piotr Cieplak3

1Université de Picardie Jules Verne - Faculté de Pharmacie & UMR CNRS 6219, 2Université de Picardie Jules Verne, Amiens, France and 3Burnham Institute for Medical Research, La Jolla, CA, USA

* To whom correspondence should be addressed. Tel: +33 3 2282 7498; Fax: +33 3 2282 7469; Email: fyd{at}q4md-forcefieldtools.org Correspondence may also be addressed to Piotr Cieplak. Tel: +1 858 646 3100; Fax: +1 858 713 9949; Email: pcieplak{at}q4md-forcefieldtools.org

Received September 1, 2007. Revised October 1, 2007. Accepted October 2, 2007.

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications.


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