Literature DB >> 11297935

Macromolecular electrostatics: continuum models and their growing pains.

T Simonson1.   

Abstract

Theoretical understanding of macromolecular electrostatics has advanced substantially over the past year. Continuum models have given promising results for calculating protein-ligand binding free energy differences, as well as pK(a)s and redox properties, particularly with explicit treatment of multiple conformers. Generalized Born and other techniques have led to the first molecular dynamics simulations of proteins and RNA with continuum solvent. Continuum and microscopic descriptions of dielectric relaxation have been critically compared.

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Year:  2001        PMID: 11297935     DOI: 10.1016/s0959-440x(00)00197-4

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


  58 in total

1.  Gaussian fluctuations and linear response in an electron transfer protein.

Authors:  Thomas Simonson
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-14       Impact factor: 11.205

2.  The pH-dependent stability of wild-type and mutant transthyretin oligomers.

Authors:  S Skoulakis; J M Goodfellow
Journal:  Biophys J       Date:  2003-05       Impact factor: 4.033

3.  Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework.

Authors:  Jeremy L England; Vijay S Pande
Journal:  Biochem Cell Biol       Date:  2010-04       Impact factor: 3.626

4.  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

5.  Protocol for MM/PBSA molecular dynamics simulations of proteins.

Authors:  Federico Fogolari; Alessandro Brigo; Henriette Molinari
Journal:  Biophys J       Date:  2003-07       Impact factor: 4.033

6.  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

7.  Influence of the solvent structure on the electrostatic interactions in proteins.

Authors:  Alexander Rubinstein; Simon Sherman
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

8.  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

9.  Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors:  Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

10.  Multiscale geometric modeling of macromolecules I: Cartesian representation.

Authors:  Kelin Xia; Xin Feng; Zhan Chen; Yiying Tong; Guo Wei Wei
Journal:  J Comput Phys       Date:  2014-01       Impact factor: 3.553

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