Empirical free energy calculation: comparison to calorimetric data (Q36280587)

13 August 2017

Empirical free energy calculation: comparison to calorimetric data (English)

1 reference

13 August 2017

S Vajda

3

0 references

author name string

Z Weng

series ordinal

1

1 reference

PMCID

2143797

13 August 2017

C Delisi

series ordinal

2

1 reference

13 August 2017

1 September 1997

1 reference

13 August 2017

1 reference

13 August 2017

6

1 reference

13 August 2017

1976-1984

1 reference

13 August 2017

9

1 reference

On the attribution and additivity of binding energies

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Some factors in the interpretation of protein denaturation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Free energy mapping of class I MHC molecules and structural determination of bound peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Energetics of protein structure.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Computational methods to predict binding free energy in ligand-receptor complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Empirical scale of side-chain conformational entropy in protein folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Structure based prediction of protein folding intermediates

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Acquisition and use of calorimetric data for prediction of the thermodynamics of ligand-binding and folding reactions of proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Classical electrostatics in biology and chemistry

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Solvation energy in protein folding and binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Computational method for the design of enzymes with altered substrate specificity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Thermodynamics of structural stability and cooperative folding behavior in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Prediction of protein complexes using empirical free energy functions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Thermodynamics of the temperature-induced unfolding of globular proteins

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

A continuum model for protein-protein interactions: application to the docking problem.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Protein docking and complementarity

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Calculation of the free energy of association for protein complexes

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation.

29 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.5560060918

Computational method for relative binding energies of enzyme-substrate complexes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Atomic solvation parameters in the analysis of protein-protein docking results

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Structural energetics of peptide recognition: Angiotensin II/antibody binding

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143797

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

21 October 2018

1 reference

12 December 2020

Rapid, electrostatically assisted association of proteins

1 reference

12 December 2020

Criteria that discriminate between native proteins and incorrectly folded models

1 reference

12 December 2020

Common features of protein unfolding and dissolution of hydrophobic compounds

1 reference

12 December 2020

Affinities of amino acid side chains for solvent water

1 reference

12 December 2020

The price of lost freedom: entropy of bimolecular complex formation

1 reference

12 December 2020

Primary T-cell lymphoma of the thyroid

1 reference

12 December 2020

Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.5560060918

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

PMCID

2143797