Literature DB >> 12547438

Combined quantum and molecular mechanics calculations on metalloproteins.

Ulf Ryde1.   

Abstract

The combination of quantum mechanics and molecular mechanics (QM/MM) methods is one of the most promising approaches to study the structure, function and properties of proteins. The number of QM/MM applications on metalloproteins is steadily increasing, especially studies with density functional methods on redox-active metal centres. Recent developments include new parameterised methods to treat covalent bonds between the quantum and classical systems, methods to obtain free energy from QM/MM results, and the combination of quantum chemistry and protein crystallography.

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Year:  2003        PMID: 12547438     DOI: 10.1016/s1367-5931(02)00016-9

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


  17 in total

1.  NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.

Authors:  Ya-Wen Hsiao; Torbjörn Drakenberg; Ulf Ryde
Journal:  J Biomol NMR       Date:  2005-02       Impact factor: 2.835

2.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  Q|R: quantum-based refinement.

Authors:  Min Zheng; Jeffrey R Reimers; Mark P Waller; Pavel V Afonine
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-01-01       Impact factor: 7.652

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

5.  Solving the scalability issue in quantum-based refinement: Q|R#1.

Authors:  Min Zheng; Nigel W Moriarty; Yanting Xu; Jeffrey R Reimers; Pavel V Afonine; Mark P Waller
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-11-30       Impact factor: 7.652

6.  Spectroscopic identification of reactive porphyrin motions.

Authors:  Alexander Barabanschikov; Alexander Demidov; Minoru Kubo; Paul M Champion; J Timothy Sage; Jiyong Zhao; Wolfgang Sturhahn; E Ercan Alp
Journal:  J Chem Phys       Date:  2011-07-07       Impact factor: 3.488

7.  QM/MM X-ray refinement of zinc metalloenzymes.

Authors:  Xue Li; Seth A Hayik; Kenneth M Merz
Journal:  J Inorg Biochem       Date:  2010-01-07       Impact factor: 4.155

8.  Lessons on O2 and NO bonding to heme from ab initio multireference/multiconfiguration and DFT calculations.

Authors:  Sason Shaik; Hui Chen
Journal:  J Biol Inorg Chem       Date:  2011-03-04       Impact factor: 3.358

9.  Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Authors:  Johnny C Wu; Jean-Philip Piquemal; Robin Chaudret; Peter Reinhardt; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2010-07-13       Impact factor: 6.006

10.  The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

Authors:  Kristina Nilsson; Hans-Petter Hersleth; Thomas H Rod; K Kristoffer Andersson; Ulf Ryde
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

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