(Q42776053)

7 November 2017

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks (English)

1 reference

Shina Caroline Lynn Kamerlin

7 November 2017

series ordinal

2

1 reference

7 November 2017

3

Arieh Warshel

1 reference

7 November 2017

Nikolay V Plotnikov

1

1 reference

PMCID

3124314

7 November 2017

language of work or name

English

0 references

publication date

27 May 2011

1 reference

Journal of Physical Chemistry B

7 November 2017

1 reference

7 November 2017

115

1 reference

7 November 2017

7950-7962

1 reference

7 November 2017

24

1 reference

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

7 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Chemically accurate coarse graining of double-stranded DNA.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Enzyme millisecond conformational dynamics do not catalyze the chemical step

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

On the relationship between folding and chemical landscapes in enzyme catalysis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

On the relationship between thermal stability and catalytic power of enzymes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Escaping free-energy minima

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Computer simulation of protein folding

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

On the energetics of ATP hydrolysis in solution

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Exploring intramolecular reactions in complex systems with metadynamics: the case of the malonate anions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

Exploring the origin of the ion selectivity of the KcsA potassium channel

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124314

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

16 August 2018

1 reference

12 December 2020

Quantum mechanical free energy barrier for an enzymatic reaction

1 reference

12 December 2020

Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics

1 reference

12 December 2020

The energy gap as a universal reaction coordinate for the simulation of chemical reactions

1 reference

12 December 2020

Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP201217B

Optimization of parameters for semiempirical methods I. Method

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP201217B

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP201217B

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP201217B

Optimization of parameters for semiempirical methods II. Applications

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP201217B

Identifiers

DOI

10.1021/JP201217B

1 reference

7 November 2017

1 reference

7 November 2017

1 reference

PMCID

3124314