Literature DB >> 17307018

QM/MM studies of enzymes.

Hans Martin Senn1, Walter Thiel.   

Abstract

Combined quantum-mechanics/molecular-mechanics (QM/MM) methods are making rapid progress both methodologically and with respect to their range of application. Mechanistic studies on enzymes, including contributions towards the understanding of enzyme catalysis, continue to be a major target. They are joined by calculations of pK(a) values, redox properties, ground- and excited-state spectroscopic parameters, and excited-state dynamics. Methodological advances include improved QM/MM schemes, in particular new approaches for an effective treatment of the QM-MM electrostatic interactions, and the incorporation of new efficient and accurate QM methods in QM/MM schemes.

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Year:  2007        PMID: 17307018     DOI: 10.1016/j.cbpa.2007.01.684

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  57 in total

1.  Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor.

Authors:  Kshatresh Dutta Dubey; Rajendra Prasad Ojha
Journal:  J Biol Phys       Date:  2010-09-02       Impact factor: 1.365

Review 2.  Single-molecule force spectroscopy approach to enzyme catalysis.

Authors:  Jorge Alegre-Cebollada; Raul Perez-Jimenez; Pallav Kosuri; Julio M Fernandez
Journal:  J Biol Chem       Date:  2010-04-09       Impact factor: 5.157

3.  Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2015-12-21       Impact factor: 3.488

4.  Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse.

Authors:  Lalith Perera; Bret D Freudenthal; William A Beard; David D Shock; Lee G Pedersen; Samuel H Wilson
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

Review 5.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

6.  GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

Authors:  José Fernando R Bachega; Luís Fernando S M Timmers; Lucas Assirati; Leonardo R Bachega; Martin J Field; Troy Wymore
Journal:  J Comput Chem       Date:  2013-09-30       Impact factor: 3.376

7.  Introduction. Biomolecular simulation.

Authors:  Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 8.  Investigating the mechanisms of photosynthetic proteins using continuum electrostatics.

Authors:  G Matthias Ullmann; Edda Kloppmann; Timm Essigke; Eva-Maria Krammer; Astrid R Klingen; Torsten Becker; Elisa Bombarda
Journal:  Photosynth Res       Date:  2008-05-14       Impact factor: 3.573

9.  Structure of the cyanobacterial phytochrome 2 photosensor implies a tryptophan switch for phytochrome signaling.

Authors:  Katrin Anders; Grazia Daminelli-Widany; Maria Andrea Mroginski; David von Stetten; Lars-Oliver Essen
Journal:  J Biol Chem       Date:  2013-10-30       Impact factor: 5.157

10.  Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

Authors:  Ganglong Cui; Weitao Yang
Journal:  J Chem Phys       Date:  2011-05-28       Impact factor: 3.488

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