R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
Open Access
- 23 December 2007
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 36 (Database) , D360-D367
- https://doi.org/10.1093/nar/gkm887
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.Keywords
This publication has 41 references indexed in Scilit:
- Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ ConformersBiophysical Journal, 2007
- Molecular Dynamics: Survey of Methods for Simulating the Activity of ProteinsChemical Reviews, 2006
- Differential Solvation and Tautomer Stability of a Model Base Pair within the Minor and Major Grooves of DNAJournal of the American Chemical Society, 2005
- Development and testing of a general amber force fieldJournal of Computational Chemistry, 2004
- A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculationsJournal of Computational Chemistry, 2003
- Solvated ensemble averaging in the calculation of partial atomic chargesJournal of Computational Chemistry, 2001
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvationJournal of the American Chemical Society, 1993
- A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelThe Journal of Physical Chemistry, 1993
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983