Literature DB >> 11352713

Large-scale ab initio quantum chemical calculations on biological systems.

R A Friesner1, B D Dunietz.   

Abstract

In this Account we describe recent advances in two ab initio electronic structure methods, localized perturbation approaches and density functional theory, that allow accurate calculations including electron correlation to be carried out for systems with hundreds of atoms. Application of these methods to large-scale modeling of biological systems is discussed. Localized perturbation methods are best suited to computation of conformational energetics and nonbonded interactions: determination of the relative energetics of various conformations of the alanine tetrapetide is presented. Density functional theory is the method of choice for studying reactive chemistry; investigations of the catalytic cycle of the enzyme methane monooxygenase are reviewed.

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Year:  2001        PMID: 11352713     DOI: 10.1021/ar980111r

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  8 in total

1.  Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations.

Authors:  Philip Shemella; Brian Pereira; Yiming Zhang; Patrick Van Roey; Georges Belfort; Shekhar Garde; Saroj K Nayak
Journal:  Biophys J       Date:  2006-11-03       Impact factor: 4.033

2.  Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study.

Authors:  David Rinaldo; Dean M Philipp; Stephen J Lippard; Richard A Friesner
Journal:  J Am Chem Soc       Date:  2007-02-28       Impact factor: 15.419

3.  Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome.

Authors:  Zuojun Guo; Meghan Gibson; Sanyasi Sitha; Steven Chu; Udayan Mohanty
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-22       Impact factor: 11.205

4.  Performance comparison of computational methods for modeling alpha-helical structures.

Authors:  Alexandru Lupan; Attila-Zsolt Kun; Francisco Carrascoza; Radu Silaghi-Dumitrescu
Journal:  J Mol Model       Date:  2012-07-31       Impact factor: 1.810

Review 5.  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

Review 6.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

7.  Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum.

Authors:  Shiru Jia; Zhiwen Mo; Yujie Dai; Xiuli Zhang; Hongjiang Yang; Yuhua Qi
Journal:  Int J Mol Sci       Date:  2009-07-29       Impact factor: 6.208

8.  A molecular fragment cheminformatics roadmap for mesoscopic simulation.

Authors:  Andreas Truszkowski; Mirco Daniel; Hubert Kuhn; Stefan Neumann; Christoph Steinbeck; Achim Zielesny; Matthias Epple
Journal:  J Cheminform       Date:  2014-10-04       Impact factor: 5.514

  8 in total

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