(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

1 reference

Journal of Molecular Recognition

15 September 2017

1 reference

15 September 2017

23

1 reference

15 September 2017

2

1 reference

15 September 2017

153-172

1 reference

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