QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase (Q37010676)

17 August 2017

QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase (English)

1 reference

17 August 2017

Hao Hu

1

1 reference

PMCID

2600730

17 August 2017

Zhenyu Lu

series ordinal

2

1 reference

PMCID

2600730

17 August 2017

Weitao Yang

series ordinal

3

1 reference

17 August 2017

1 March 2007

1 reference

Journal of Chemical Theory and Computation

17 August 2017

1 reference

17 August 2017

3

1 reference

17 August 2017

2

1 reference

17 August 2017

390-406

1 reference

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

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Tracing the minimum-energy path on the free-energy surface

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Direct determination of reaction paths and stationary points on potential of mean force surfaces

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Why does the Ras switch "break" by oncogenic mutations?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

How enzymes work: analysis by modern rate theory and computer simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Computer simulations of enzyme catalysis: methods, progress, and insights

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Quantum mechanical methods for enzyme kinetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Enzyme dynamics during catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Triosephosphate isomerase: a theoretical comparison of alternative pathways

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Reaction coordinates of biomolecular isomerization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Quadratic string method for determining the minimum-energy path based on multiobjective optimization

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600730

A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells

4 September 2018

1 reference

12 December 2020

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.

1 reference

12 December 2020

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

1 reference

12 December 2020

Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes

1 reference

12 December 2020

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

1 reference

12 December 2020

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase

1 reference

12 December 2020

Optimizing the structures of minimum and transition state on the free energy surface

1 reference

12 December 2020

QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction

1 reference

12 December 2020

Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase

1 reference

12 December 2020

Energy landscape of a native protein: jumping-among-minima model

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT600240Y

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

PMCID

2600730