(Q41999691)

15 October 2017

On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions (English)

1 reference

15 October 2017

N Froloff

1

1 reference

PMCID

2143728

15 October 2017

A Windemuth

series ordinal

2

1 reference

PMCID

2143728

15 October 2017

B Honig

series ordinal

3

1 reference

15 October 2017

1 June 1997

1 reference

15 October 2017

1 reference

15 October 2017

6

1 reference

15 October 2017

1293-1301

1 reference

15 October 2017

6

1 reference

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

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Hydrogen bonding stabilizes globular proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Side-chain conformational entropy in protein folding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

A free energy analysis of nucleic acid base stacking in aqueous solution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Empirical scale of side-chain conformational entropy in protein folding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Toward an estimation of binding constants in aqueous solution: studies of associations of vancomycin group antibiotics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Alloantibodies can discriminate class I major histocompatibility complex molecules associated with various endogenous peptides

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Peptide-induced conformational changes in class I molecules. Direct detection by flow cytometry.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Evaluation of the conformational free energies of loops in proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Biophysical tools for structure-based drug design

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann method

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Protein-peptide interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Free energy determinants of secondary structure formation: I. alpha-Helices

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Ranking potential binding peptides to MHC molecules by a computational threading approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Analysis of the structure of empty and peptide-loaded major histocompatibility complex molecules at the cell surface

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Functional group contributions to drug-receptor interactions.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

The interpretation of protein structures: Estimation of static accessibility

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Computer-aided molecular design

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Co-operativity in protein-protein association. The structure and stability of the actin filament

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Hydrogen bond stereochemistry in protein structure and function

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Electrostatic interactions in macromolecules: theory and applications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Peptide-induced conformational change of the class I heavy chain

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

23 Theoretical calculations of relative affinities of binding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Peptide-induced conformational changes in class I heavy chains alter major histocompatibility complex recognition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Major histocompatibility complex conformational epitopes are peptide specific

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

The Protein Data Bank: a computer-based archival file for macromolecular structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Areas, volumes, packing and protein structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

Computational method for relative binding energies of enzyme-substrate complexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143728

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

18 August 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560060617

Entropy changes accompanying association reactions of proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9194189

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9194189

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9194189

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.5560060617

1 reference

15 October 2017

1 reference

15 October 2017

1 reference

PMCID

2143728