Entropy and free energy of a mobile protein loop in explicit water (Q42140475)

17 October 2017

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

1 reference

17 October 2017

Srinath Cheluvaraja

1

1 reference

17 October 2017

Mihail Mihailescu

series ordinal

2

1 reference

17 October 2017

Hagai Meirovitch

series ordinal

3

1 reference

17 October 2017

language of work or name

English

0 references

publication date

10 July 2008

1 reference

Journal of Physical Chemistry B

17 October 2017

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17 October 2017

112

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17 October 2017

31

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17 October 2017

9512-9522

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Minimalist explicit solvation models for surface loops in proteins

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Intrinsic dynamics of an enzyme underlies catalysis

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Structure of human salivary alpha-amylase at 1.6 A resolution: implications for its role in the oral cavity

29 May 2018

1 reference

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Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.

29 May 2018

1 reference

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Structural basis of α-amylase activation by chloride

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Probing the role of the chloride ion in the mechanism of human pancreatic alpha-amylase

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Protein hydration elucidated by molecular dynamics simulation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

The allosteric activation of mammalian alpha-amylase by chloride.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

The metal specificity of mammalian α-amylase as revealed by enzyme activity and structural probes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

Dynamics of folded proteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671085

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

17 August 2018

1 reference

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

17 August 2018

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

Evaluating the Accuracy of the Quasiharmonic Approximation

1 reference

12 December 2020

Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil

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

Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution

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

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

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP801827F

1 reference

17 October 2017

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17 October 2017

1 reference