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

Dupradeau FY, Cézard C, Lelong R, Stanislawiak E, Pêcher J, Delepine JC, Cieplak P - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Université de Picardie Jules Verne - Faculté de Pharmacie & UMR CNRS 6219, Université de Picardie Jules Verne, Amiens, France.

ABSTRACT
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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General overview of the R.E.DD.B. home page.
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Figure 1: General overview of the R.E.DD.B. home page.

Mentions: R.E.DD.B. presently stores force field topologies for around 150 molecular systems, covering a vast area of relevant biological applications, divided into two sub-entities, namely ‘Whole molecule’ and ‘Molecule fragment’. An overview of the R.E.DD.B. home page is presented in Figure 1.


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

Dupradeau FY, Cézard C, Lelong R, Stanislawiak E, Pêcher J, Delepine JC, Cieplak P - Nucleic Acids Res. (2007)

General overview of the R.E.DD.B. home page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238896&req=5

Figure 1: General overview of the R.E.DD.B. home page.
Mentions: R.E.DD.B. presently stores force field topologies for around 150 molecular systems, covering a vast area of relevant biological applications, divided into two sub-entities, namely ‘Whole molecule’ and ‘Molecule fragment’. An overview of the R.E.DD.B. home page is presented in Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Université de Picardie Jules Verne - Faculté de Pharmacie & UMR CNRS 6219, Université de Picardie Jules Verne, Amiens, France.

ABSTRACT
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.

Show MeSH