Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions (Q46358954)

21 December 2017

title

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions (English)

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21 December 2017

Edina Rosta

1

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Arieh Warshel

series ordinal

3

object named as

Arieh Warshel

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21 December 2017

Marco Klähn

2

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21 December 2017

language of work or name

English

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publication date

1 February 2006

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21 December 2017

Journal of Physical Chemistry B

published in

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21 December 2017

volume

110

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21 December 2017

issue

6

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21 December 2017

page(s)

2934-2941

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21 December 2017

Dual-topology/dual-coordinate free-energy simulation using QM/MM force field

cites work

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Comparison of formation of reactive conformers for the SN2 displacements by CH3CO2- in water and by Asp124-CO2- in a haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Simulating enzyme reactions: challenges and perspectives

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Nonenzymatic and enzymatic hydrolysis of alkyl halides: a theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

A view at the millennium: the efficiency of enzymatic catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Chlorine kinetic isotope effects on enzymatic dehalogenations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Evaluation of catalytic free energies in genetically modified proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Quantum mechanical calculations on biological systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Quantum mechanical free energy barrier for an enzymatic reaction

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Dynamics of biochemical and biophysical reactions: insight from computer simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Steady-state and pre-steady-state kinetic analysis of halopropane conversion by a rhodococcus haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

How much do enzymes really gain by restraining their reacting fragments?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Histidine 289 is essential for hydrolysis of the alkyl-enzyme intermediate of haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Accelerating quantum mechanical/molecular mechanical sampling using pure molecular mechanical potential as an importance function: the case of effective fragment potential

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP057109J

Identifiers

DOI

10.1021/JP057109J

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21 December 2017

1 reference

21 December 2017