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On the electrostatic component of protein-protein binding free energy.

Talley K, Ng C, Shoppell M, Kundrotas P, Alexov E.

PMC Biophys. 2008 Nov 5;1(1):2.PMID: 19351424 [PubMed - in process]Related articlesFree article

Optimization of electrostatic interactions in protein-protein complexes.

Brock K, Talley K, Coley K, Kundrotas P, Alexov E.

Biophys J. 2007 Nov 15;93(10):3340-52. Epub 2007 Aug 10.PMID: 17693468 [PubMed - indexed for MEDLINE]Related articlesFree article

Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models.

Leontyev IV, Stuchebrukhov AA.

J Chem Phys. 2009 Feb 28;130(8):085103.PMID: 19256628 [PubMed - indexed for MEDLINE]Related articlesFree article

Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations.

Kaminski GA, Ponomarev SY, Liu AB.

J Chem Theory Comput. 2009 Oct 5;5(11):2935-2943.PMID: 20209038 [PubMed]Related articles

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.

Bertonati C, Honig B, Alexov E.

Biophys J. 2007 Mar 15;92(6):1891-9. Epub 2007 Jan 5.PMID: 17208980 [PubMed - indexed for MEDLINE]Related articlesFree article

Binding affinity prediction with different force fields: examination of the linear interaction energy method.

Almlöf M, Brandsdal BO, Aqvist J.

J Comput Chem. 2004 Jul 30;25(10):1242-54.PMID: 15139037 [PubMed]Related articles

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.

J Chem Inf Model. 2007 Jan-Feb;47(1):122-33.PMID: 17238257 [PubMed - indexed for MEDLINE]Related articles

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603.

Lee FS, Chu ZT, Bolger MB, Warshel A.

Protein Eng. 1992 Apr;5(3):215-28.PMID: 1409541 [PubMed - indexed for MEDLINE]Related articles

On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations.

Rankin KN, Sulea T, Purisima EO.

J Comput Chem. 2003 Jun;24(8):954-62.PMID: 12720316 [PubMed]Related articles

Calculation of protein-ligand binding free energy by using a polarizable potential.

Jiao D, Golubkov PA, Darden TA, Ren P.

Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6290-5. Epub 2008 Apr 21.PMID: 18427113 [PubMed - indexed for MEDLINE]Related articlesFree article

Polarization and polarizability assessed by protein amide acidity.

Hernández G, Anderson JS, LeMaster DM.

Biochemistry. 2009 Jul 14;48(27):6482-94.PMID: 19507827 [PubMed - indexed for MEDLINE]Related articles

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

Marenich AV, Cramer CJ, Truhlar DG.

J Phys Chem B. 2009 May 7;113(18):6378-96.PMID: 19366259 [PubMed]Related articles

Direct calculation of the binding free energies of FKBP ligands.

Fujitani H, Tanida Y, Ito M, Jayachandran G, Snow CD, Shirts MR, Sorin EJ, Pande VS.

J Chem Phys. 2005 Aug 22;123(8):084108.PMID: 16164283 [PubMed - indexed for MEDLINE]Related articles

Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects.

Hwang MJ, Ni X, Waldman M, Ewig CS, Hagler AT.

Biopolymers. 1998 May;45(6):435-68. Review.PMID: 9538697 [PubMed - indexed for MEDLINE]Related articles

Mean-field analysis of protein-protein interactions.

Olson MA.

Biophys Chem. 1998 Nov 16;75(2):115-28.PMID: 17027458 [PubMed]Related articles

Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation.

Deng NJ, Cieplak P.

Phys Chem Chem Phys. 2009 Jul 7;11(25):4968-81. Epub 2009 Apr 2.PMID: 19562127 [PubMed - indexed for MEDLINE]Related articles

Computational analysis of the binding of P1 variants of domain 3 of turkey ovomucoid inhibitor to Streptomyces griseus protease B.

Fujinaga M, Huang K, Bateman KS, James MN.

J Mol Biol. 1998 Dec 18;284(5):1683-94.PMID: 9878379 [PubMed - indexed for MEDLINE]Related articles

Continuum polarizable force field within the Poisson-Boltzmann framework.

Tan YH, Tan C, Wang J, Luo R.

J Phys Chem B. 2008 Jun 26;112(25):7675-88. Epub 2008 May 29.PMID: 18507452 [PubMed - indexed for MEDLINE]Related articlesFree article

Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes.

Grootenhuis PD, van Galen PJ.

Acta Crystallogr D Biol Crystallogr. 1995 Jul 1;51(Pt 4):560-6.PMID: 15299844 [PubMed]Related articles

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues.

Xu Z, Luo HH, Tieleman DP.

J Comput Chem. 2007 Feb;28(3):689-97.PMID: 17195160 [PubMed - in process]Related articles