Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics (Q39958434)

15 September 2017

Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics (English)

1 reference

15 September 2017

Hagai Meirovitch

1

1 reference

PMC publication ID

2823937

15 September 2017

language of work or name

1 reference

1 March 2010

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Journal of Molecular Recognition

15 September 2017

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15 September 2017

23

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15 September 2017

2

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15 September 2017

153-172

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

15 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Calculation of protein-ligand binding affinities.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Biomolecular modeling: Goals, problems, perspectives

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Simulation method for calculating the entropy and free energy of peptides and proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

The statistical-thermodynamic basis for computation of binding affinities: a critical review

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

New theoretical methodology for elucidating the solution structure of peptides from NMR data. II. Free energy of dominant microstates of Leu-enkephalin and population-weighted average nuclear Overhauser effects intensities

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Computer simulation of the free energy of peptides with the local states method: analogues of gonadotropin releasing hormone in the random coil and stable states

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Free energy via molecular simulation: applications to chemical and biomolecular systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Dynamics of folded proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Entropy and free energy of a mobile protein loop in explicit water

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Calculation of the Entropy of Lattice Polymer Models from Monte Carlo Trajectories

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Structural evidence for induced fit as a mechanism for antibody-antigen recognition

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Evaluating the Accuracy of the Quasiharmonic Approximation

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Estimation of absolute solvent and solvation shell entropies via permutation reduction.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Concepts in receptor optimization: targeting the RGD peptide.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: a Monte Carlo-generalized Born model study

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Tork: Conformational analysis method for molecules and complexes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2823937

Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model

20 August 2018

1 reference

12 December 2020

Absolute and relative entropies from computer simulation with applications to ligand binding

1 reference

12 December 2020

Packing structures and transitions in liquids and solids

1 reference

12 December 2020

Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

1 reference

12 December 2020

Stability of polypeptide conformational states as determined by computer simulation of the free energy

1 reference

12 December 2020

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

1 reference

12 December 2020

Mechanisms of antibody binding to a protein

1 reference

12 December 2020

Backbone entropy of loops as a measure of their flexibility: application to a ras protein simulated by molecular dynamics

1 reference

12 December 2020

Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks

1 reference

12 December 2020

Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions

1 reference

12 December 2020

An optimized harmonic reference system for the evaluation of discretized path integrals

1 reference

19 October 2022

https://opencitations.net/index/coci/api/v1/citations/10.1063/1.447232

Identifiers

DOI

10.1002/JMR.973

1 reference

15 September 2017

1 reference

PMC publication ID

2823937

15 September 2017

PubMed publication ID

19650071

1 reference

PMC publication ID

2823937