Literature DB >> 2072125

The inclusion of electrostatic hydration energies in molecular mechanics calculations.

M K Gilson1, B Honig.   

Abstract

The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.

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Year:  1991        PMID: 2072125     DOI: 10.1007/BF00173467

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  19 in total

Review 1.  Electrostatic interactions in macromolecules: theory and applications.

Authors:  K A Sharp; B Honig
Journal:  Annu Rev Biophys Biophys Chem       Date:  1990

2.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

3.  Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis.

Authors:  M K Gilson; B Honig
Journal:  Proteins       Date:  1988

4.  The dielectric constant of a folded protein.

Authors:  M K Gilson; B H Honig
Journal:  Biopolymers       Date:  1986-11       Impact factor: 2.505

5.  Computer simulations of the diffusion of a substrate to an active site of an enzyme.

Authors:  K Sharp; R Fine; B Honig
Journal:  Science       Date:  1987-06-12       Impact factor: 47.728

6.  Prediction of electrostatic effects of engineering of protein charges.

Authors:  M J Sternberg; F R Hayes; A J Russell; P G Thomas; A R Fersht
Journal:  Nature       Date:  1987 Nov 5-11       Impact factor: 49.962

7.  Calculation of electrostatic potentials in an enzyme active site.

Authors:  M K Gilson; B H Honig
Journal:  Nature       Date:  1987 Nov 5-11       Impact factor: 49.962

8.  Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur.

Authors:  Wayne A Hendrickson; Martha M Teeter
Journal:  Nature       Date:  1981-03-12       Impact factor: 49.962

9.  Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains.

Authors:  J H Ploegman; G Drent; K H Kalk; W G Hol
Journal:  J Mol Biol       Date:  1978-08-25       Impact factor: 5.469

10.  Solvent-accessible surfaces of proteins and nucleic acids.

Authors:  M L Connolly
Journal:  Science       Date:  1983-08-19       Impact factor: 47.728

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  25 in total

1.  H-bonding in protein hydration revisited.

Authors:  Michael Petukhov; Georgy Rychkov; Leonid Firsov; Luis Serrano
Journal:  Protein Sci       Date:  2004-07-06       Impact factor: 6.725

2.  Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.

Authors:  Wei Chen; Chia-En Chang; Michael K Gilson
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

3.  Molecular modeling of nucleic acid structure: electrostatics and solvation.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-08

4.  Influence of a channel-forming peptide on energy barriers to ion permeation, viewed from a continuum dielectric perspective.

Authors:  M B Partenskii; V Dorman; P C Jordan
Journal:  Biophys J       Date:  1994-10       Impact factor: 4.033

5.  Improving the desolvation penalty in empirical protein pKa modeling.

Authors:  Mats H M Olsson
Journal:  J Mol Model       Date:  2011-06-14       Impact factor: 1.810

6.  The physical basis of nucleic acid base stacking in water.

Authors:  R Luo; H S Gilson; M J Potter; M K Gilson
Journal:  Biophys J       Date:  2001-01       Impact factor: 4.033

7.  Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Authors:  Crystal N Nguyen; Tom Kurtzman Young; Michael K Gilson
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

8.  New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations.

Authors:  Sarvin Moghaddam; Cheng Yang; Mikhail Rekharsky; Young Ho Ko; Kimoon Kim; Yoshihisa Inoue; Michael K Gilson
Journal:  J Am Chem Soc       Date:  2011-02-22       Impact factor: 15.419

9.  Folding simulations of alanine-based peptides with lysine residues.

Authors:  S S Sung
Journal:  Biophys J       Date:  1995-03       Impact factor: 4.033

10.  Monte Carlo simulations of beta-hairpin folding at constant temperature.

Authors:  S S Sung
Journal:  Biophys J       Date:  1999-01       Impact factor: 4.033

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