Literature DB >> 15911753

A quantum mechanical polarizable force field for biomolecular interactions.

A G Donchev1, V D Ozrin, M V Subbotin, O V Tarasov, V I Tarasov.   

Abstract

We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs.

Entities:  

Year:  2005        PMID: 15911753      PMCID: PMC1142387          DOI: 10.1073/pnas.0502962102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  5 in total

Review 1.  Polarizable force fields.

Authors:  T A Halgren; W Damm
Journal:  Curr Opin Struct Biol       Date:  2001-04       Impact factor: 6.809

2.  Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.

Authors:  George A Kaminski; Harry A Stern; B J Berne; Richard A Friesner; Yixiang X Cao; Robert B Murphy; Ruhong Zhou; Thomas A Halgren
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

Authors:  A Warshel; M Levitt
Journal:  J Mol Biol       Date:  1976-05-15       Impact factor: 5.469

4.  Water polarizability in condensed phase: ab initio evaluation by cluster approach.

Authors:  Akihiro Morita
Journal:  J Comput Chem       Date:  2002-11-30       Impact factor: 3.376

5.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

  5 in total
  18 in total

1.  Molecular simulation methods in drug discovery: a prospective outlook.

Authors:  Xavier Barril; F Javier Luque
Journal:  J Comput Aided Mol Des       Date:  2011-12-08       Impact factor: 3.686

2.  Water properties from first principles: simulations by a general-purpose quantum mechanical polarizable force field.

Authors:  A G Donchev; N G Galkin; A A Illarionov; O V Khoruzhii; M A Olevanov; V D Ozrin; M V Subbotin; V I Tarasov
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-24       Impact factor: 11.205

3.  Near-native structure refinement using in vacuo energy minimization.

Authors:  Christopher M Summa; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-20       Impact factor: 11.205

4.  Application of a polarizable force field to calculations of relative protein-ligand binding affinities.

Authors:  Oleg Khoruzhii; Alexander G Donchev; Nikolay Galkin; Alexei Illarionov; Mikhail Olevanov; Vladimir Ozrin; Cary Queen; Vladimir Tarasov
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-24       Impact factor: 11.205

Review 5.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

6.  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

7.  Remarkable patterns of surface water ordering around polarized buckminsterfullerene.

Authors:  Gaurav Chopra; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-15       Impact factor: 11.205

Review 8.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

9.  Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.

Authors:  Zhenyu Lu; Nengjie Zhou; Qin Wu; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2011-12-13       Impact factor: 6.006

10.  Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

Authors:  Igor V Leontyev; Alexei A Stuchebrukhov
Journal:  J Chem Phys       Date:  2014-07-07       Impact factor: 3.488

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