R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries.
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.
21 references, click to expand
-
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.J Chem Theory Comput. 2005 Jan;1(1):153-68 PMID: 26641126
-
Molecular mechanics parameters for the FapydG DNA lesion.J Comput Chem. 2008 Jan 15;29(1):17-23 PMID: 17551974
-
Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates.Theochem. 2000 Aug;527(1-3):149-156 PMID: 25309012
-
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.J Am Chem Soc. 1988 Mar 1;110(6):1657-66 PMID: 27557051
-
Applications of Computational Chemistry to the Study of Cyclodextrins.Chem Rev. 1998 Jul 30;98(5):1829-1874 PMID: 11848951
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins.J Phys Chem B. 1998 Apr 30;102(18):3586-616 PMID: 24889800
-
Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals.J Am Chem Soc. 1974 Aug 21;96(17):5319-27 PMID: 4851860
-
Differential solvation and tautomer stability of a model base pair within the minor and major grooves of DNA.J Am Chem Soc. 2005 Nov 9;127(44):15612-7 PMID: 16262427
-
Expanding the genetic code of Escherichia coli.Science. 2001 Apr 20;292(5516):498-500 PMID: 11313494
-
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.J Comput Chem. 2004 Oct;25(13):1656-76 PMID: 15264259
-
Computational carbohydrate chemistry: what theoretical methods can tell us.Glycoconj J. 1998 Mar;15(3):209-16 PMID: 9579797
-
Quantum mechanical study of the nonbonded forces in water-methanol complexes.J Phys Chem A. 2001 Apr 26;105(16):4150-5 PMID: 16518456
-
Molecular dynamics: survey of methods for simulating the activity of proteins.Chem Rev. 2006 May;106(5):1589-615 PMID: 16683746
-
Development and testing of a general amber force field.J Comput Chem. 2004 Jul 15;25(9):1157-74 PMID: 15116359
-
Protein folding-simulation.Chem Rev. 2006 May;106(5):1898-916 PMID: 16683760
-
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.Biophys J. 2007 Jun 1;92(11):3817-29 PMID: 17351000
-
An improved nucleic acid parameter set for the GROMOS force field.J Comput Chem. 2005 May;26(7):725-37 PMID: 15770662
-
Solvent interactions determine carbohydrate conformation.Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10541-5 PMID: 11526221
-
Solvated ensemble averaging in the calculation of partial atomic charges.J Comput Chem. 2001 Aug;22(11):1125-37 PMID: 17882310
-
Chemical markup, XML, and the World Wide Web. 4. CML schema.J Chem Inf Comput Sci. 2003 May-Jun;43(3):757-72 PMID: 12767134
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.J Comput Chem. 2003 Dec;24(16):1999-2012 PMID: 14531054
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