Literature DB >> 11297931

New developments in applying quantum mechanics to proteins.

V Gogonea1, D Suárez, A van der Vaart, K M Merz.   

Abstract

Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.

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Year:  2001        PMID: 11297931     DOI: 10.1016/s0959-440x(00)00193-7

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


  10 in total

1.  Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle.

Authors:  Shigehiko Hayashi; Emad Tajkhorshid; Klaus Schulten
Journal:  Biophys J       Date:  2002-09       Impact factor: 4.033

Review 2.  Quantum chemical studies of protein structure.

Authors:  Eric Oldfield
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2005-06-29       Impact factor: 6.237

3.  Energy analysis of chemistry for correct insertion by DNA polymerase beta.

Authors:  Ping Lin; Lars C Pedersen; Vinod K Batra; William A Beard; Samuel H Wilson; Lee G Pedersen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-28       Impact factor: 11.205

Review 4.  Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.

Authors:  M R Gunner; Junjun Mao; Yifan Song; Jinrang Kim
Journal:  Biochim Biophys Acta       Date:  2006-06-17

5.  Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes.

Authors:  Yue Yang; Michael N Weaver; Kenneth M Merz
Journal:  J Phys Chem A       Date:  2009-09-10       Impact factor: 2.781

6.  Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics.

Authors:  Monique Laberge; Takashi Yonetani
Journal:  Biophys J       Date:  2007-12-20       Impact factor: 4.033

7.  A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.

Authors:  Timothy J Giese; Haoyuan Chen; Thakshila Dissanayake; George M Giambaşu; Hugh Heldenbrand; Ming Huang; Erich R Kuechler; Tai-Sung Lee; Maria T Panteva; Brian K Radak; Darrin M York
Journal:  J Chem Theory Comput       Date:  2013-03-12       Impact factor: 6.006

8.  Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus.

Authors:  Ivan Tubert-Brohman; Cristiano Ruch Werneck Guimarães; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2005       Impact factor: 6.006

9.  AM1* parameters for phosphorus, sulfur and chlorine.

Authors:  Paul Winget; Anselm H C Horn; Cenk Selçuki; Bodo Martin; Timothy Clark
Journal:  J Mol Model       Date:  2003-09-04       Impact factor: 1.810

10.  Using quantum mechanical approaches to study biological systems.

Authors:  Kenneth M Merz
Journal:  Acc Chem Res       Date:  2014-06-06       Impact factor: 22.384

  10 in total

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