Calculation of free-energy differences by confinement simulations. Application to peptide conformers (Q37010049)

17 August 2017

Calculation of free-energy differences by confinement simulations. Application to peptide conformers (English)

1 reference

17 August 2017

M Cecchini

1

0 references

Martin Karplus

series ordinal

4

object named as

M Karplus

1 reference

17 August 2017

S V Krivov

2

1 reference

17 August 2017

M Spichty

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

1 July 2009

1 reference

Journal of Physical Chemistry B

17 August 2017

1 reference

17 August 2017

113

1 reference

17 August 2017

29

1 reference

17 August 2017

9728-9740

1 reference

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Diffusive reaction dynamics on invariant free energy profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Allostery and cooperativity revisited

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

A hierarchy of timescales in protein dynamics is linked to enzyme 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=3710665

Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

The dynamic energy landscape of dihydrofolate reductase 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=3710665

The molecular mechanism of muscle contraction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Long-timescale simulation methods

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Searching for new allosteric sites in enzymes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Hidden complexity of free energy surfaces for peptide (protein) folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics 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=3710665

Biomolecular motors: the F1-ATPase paradigm

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Structural mechanism of muscle contraction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Effective energy function for proteins in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Viscosity-dependent structural fluctuations in enzyme 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=3710665

Computing conformational free energy by deactivated morphing

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

A differential fluctuation theorem

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Wordom: a program for efficient analysis of molecular dynamics simulations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Absolute free-energy calculations of liquids using a harmonic reference state.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

An efficient, path-independent method for free-energy calculations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Simple estimation of absolute free energies for biomolecules.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

Brain nicotinic receptors: structure and regulation, role in learning and reinforcement

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3710665

The protein folding network

20 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19552392

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19552392

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

MECHANISM OF ENZYME CATALYSIS

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19552392

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulation of activation free energies in molecular systems

1 reference

11 October 2022

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Replica-exchange molecular dynamics method for protein folding

1 reference

11 October 2022

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

1 reference

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

1 reference

11 October 2022

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New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres

1 reference

11 October 2022

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

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Brain nicotinic receptors: structure and regulation, role in learning and reinforcement1Published on the World Wide Web on 24 October 1997.1

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP9020646

Identifiers

DOI

10.1021/JP9020646

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

19552392

1 reference