Literature DB >> 14631821

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress.

A Shurki1, A Warshel.   

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Year:  2003        PMID: 14631821     DOI: 10.1016/s0065-3233(03)66007-9

Source DB:  PubMed          Journal:  Adv Protein Chem        ISSN: 0065-3233


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  48 in total

1.  Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase.

Authors:  Marek Strajbl; Avital Shurki; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-01       Impact factor: 11.205

2.  Comparison of mode analyses at different resolutions applied to nucleic acid systems.

Authors:  Adam W Van Wynsberghe; Qiang Cui
Journal:  Biophys J       Date:  2005-08-12       Impact factor: 4.033

3.  Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.

Authors:  Mats H M Olsson; Janez Mavri; Arieh Warshel
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

4.  On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.

Authors:  Marco Klähn; Sonja Braun-Sand; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2005-08-18       Impact factor: 2.991

5.  Effects of a distal mutation on active site chemistry.

Authors:  Lin Wang; Scott Tharp; Tzvia Selzer; Stephen J Benkovic; Amnon Kohen
Journal:  Biochemistry       Date:  2006-02-07       Impact factor: 3.162

6.  Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.

Authors:  P H König; N Ghosh; M Hoffmann; M Elstner; E Tajkhorshid; Th Frauenheim; Q Cui
Journal:  J Phys Chem A       Date:  2006-01-19       Impact factor: 2.781

7.  Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin.

Authors:  Maria Andrea Mroginski; Franz Mark; Walter Thiel; Peter Hildebrandt
Journal:  Biophys J       Date:  2007-05-18       Impact factor: 4.033

8.  Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.

Authors:  Chuanyun Xiao; Yingkai Zhang
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

9.  QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.

Authors:  Hao Hu; Zhenyu Lu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

10.  The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.

Authors:  Sonja Braun-Sand; Pankaz K Sharma; Zhen T Chu; Andrei V Pisliakov; Arieh Warshel
Journal:  Biochim Biophys Acta       Date:  2008-03-14
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