Literature DB >> 15093837

Recent advances in the development and application of implicit solvent models in biomolecule simulations.

Michael Feig1, Charles L Brooks.   

Abstract

Advances have recently been made in the development of implicit solvent methodologies and their application to the modeling of biomolecules, particularly with regard to generalized Born approaches, dielectric screening function formulations and models based on solvent-accessible surface areas. Interesting new developments include more refined non-polar solvation energy estimators, and implicit methods for modeling low-dielectric and heterogeneous environments such as membrane systems. These have been successfully applied to molecular dynamics simulations, the scoring of protein conformations, and the calculation of binding affinities and folding free energy landscapes.

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Year:  2004        PMID: 15093837     DOI: 10.1016/j.sbi.2004.03.009

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  181 in total

1.  Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants.

Authors:  Bryan F Shaw; Grégory F Schneider; Haribabu Arthanari; Max Narovlyansky; Demetri Moustakas; Armando Durazo; Gerhard Wagner; George M Whitesides
Journal:  J Am Chem Soc       Date:  2011-10-13       Impact factor: 15.419

2.  Differential geometry based solvation model II: Lagrangian formulation.

Authors:  Zhan Chen; Nathan A Baker; G W Wei
Journal:  J Math Biol       Date:  2011-01-30       Impact factor: 2.259

3.  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

4.  Computational protein design is a challenge for implicit solvation models.

Authors:  Alfonso Jaramillo; Shoshana J Wodak
Journal:  Biophys J       Date:  2004-09-17       Impact factor: 4.033

5.  Evaluation of DNA Force Fields in Implicit Solvation.

Authors:  Thomas Gaillard; David A Case
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

Review 6.  Structure elucidation of dimeric transmembrane domains of bitopic proteins.

Authors:  Eduard V Bocharov; Pavel E Volynsky; Konstantin V Pavlov; Roman G Efremov; Alexander S Arseniev
Journal:  Cell Adh Migr       Date:  2010-05-01       Impact factor: 3.405

7.  A comparable study of image approximations to the reaction field.

Authors:  Shaozhong Deng; Wei Cai; Donald Jacobs
Journal:  Comput Phys Commun       Date:  2007-11-01       Impact factor: 4.390

8.  An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors:  Yuchun Lin; Andrij Baumketner; Shaozhong Deng; Zhenli Xu; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

9.  Generalized Born model with a simple, robust molecular volume correction.

Authors:  John Mongan; Carlos Simmerling; J Andrew McCammon; David A Case; Alexey Onufriev
Journal:  J Chem Theory Comput       Date:  2007-01-01       Impact factor: 6.006

10.  New Versions of Image Approximations to the Ionic Solvent Induced Reaction Field.

Authors:  Changfeng Xue; Shaozhong Deng
Journal:  Comput Phys Commun       Date:  2008-02-01       Impact factor: 4.390

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