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

François-Yves Dupradeau¹, Christine Cézard, Rodolphe Lelong

¹Université de Picardie Jules Verne - Faculté de Pharmacie & UMR CNRS 6219, Université de Picardie Jules Verne, Amiens, France.

Nucleic Acids Research

|October 27, 2007

Summary

The RESP ESP charge DataBase (R.E.DD.B.) offers a free resource for atomic charge values and force field libraries. This database supports molecular dynamics simulations for biological applications.

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Area of Science:

Computational Chemistry
Molecular Modeling
Bioinformatics

Background:

Accurate atomic charge values are crucial for molecular dynamics (MD) simulations.
Existing resources for RESP and ESP charges are fragmented and may lack comprehensive coverage.
The development of user-friendly databases is essential for advancing computational chemistry research.

Purpose of the Study:

To introduce the RESP ESP charge DataBase (R.E.DD.B.) as a novel, free online resource.
To provide a centralized repository for RESP and ESP atomic charge values and force field libraries.
To facilitate the integration of charge data into common molecular dynamics packages.

Main Methods:

Web-based database storing charge values and molecular structures in Tripos mol2 format.
Inclusion of charge derivation procedures and scripts for MD package integration.
User interface for storing and distributing charge data and force field libraries.

Main Results:

R.E.DD.B. provides effective and reproducible charge values and molecular structures.
The database includes force field libraries for molecules, fragments, and biological analogs (amino acids, nucleotides, etc.).
The first version, released in January 2006, covers a wide range of biological applications.

Conclusions:

R.E.DD.B. serves as a valuable and accessible resource for the scientific community.
The database enhances the efficiency and reproducibility of molecular dynamics simulations.
It supports research in various biological applications by providing essential force field parameters.