Literature DB >> 25880693

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States.

Elizabeth Brunk1,2, Ursula Rothlisberger1,3.   

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Year:  2015        PMID： 25880693     DOI： 10.1021/cr500628b

Source DB:  PubMed          Journal:  Chem Rev        ISSN： 0009-2665            Impact factor:   60.622


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  55 in total

Review 1.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

Review 2.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 3.  Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.

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Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

4.  Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM.

Authors:  Jia-Ning Wang; Wei Liu; Pengfei Li; Yan Mo; Wenxin Hu; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei
Journal:  J Chem Theory Comput       Date:  2021-02-16       Impact factor: 6.006

5.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

6.  Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Authors:  Milena Vujović; Mioy Huynh; Sebastian Steiner; Pablo Garcia-Fernandez; Marcus Elstner; Qiang Cui; Maja Gruden
Journal:  J Comput Chem       Date:  2018-10-09       Impact factor: 3.376

7.  COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.

Authors:  Oliver Weingart; Artur Nenov; Piero Altoè; Ivan Rivalta; Javier Segarra-Martí; Irina Dokukina; Marco Garavelli
Journal:  J Mol Model       Date:  2018-09-03       Impact factor: 1.810

Review 8.  The Need for Integrated Approaches in Metabolic Engineering.

Authors:  Anna Lechner; Elizabeth Brunk; Jay D Keasling
Journal:  Cold Spring Harb Perspect Biol       Date:  2016-11-01       Impact factor: 10.005

9.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

10.  QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.

Authors:  D Roston; Q Cui
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600
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