(Q41790879)

10 October 2017

Prediction of protein complexes using empirical free energy functions (English)

1 reference

protein function prediction

10 October 2017

0 references

S Vajda

2

0 references

author name string

Z Weng

series ordinal

1

1 reference

PMCID

2143396

10 October 2017

C Delisi

series ordinal

3

1 reference

10 October 2017

1 April 1996

1 reference

10 October 2017

1 reference

10 October 2017

5

1 reference

10 October 2017

614-626

1 reference

10 October 2017

4

1 reference

Empirical scale of side-chain conformational entropy in protein folding

10 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Binding of amino acid side chains to preformed cavities: interaction of serine proteinases with turkey ovomucoid third domains with coded and noncoded P1 residues

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Evaluation of the conformational free energies of loops in proteins.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

PUZZLE: a new method for automated protein docking based on surface shape complementarity.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Solvation energy in protein folding and binding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Excluded volume approximation to protein-solvent interaction. The solvent contact model

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

"Soft docking": matching of molecular surface cubes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Computational method for the design of enzymes with altered substrate specificity

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Protein-protein recognition analyzed by docking simulation.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Docking by least-squares fitting of molecular surface patterns

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Calculation of the free energy of association for protein complexes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Prediction of the structure of a receptor-protein complex using a binary docking method

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Atomic solvation parameters applied to molecular dynamics of proteins in solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

Principles of protein-protein recognition

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143396

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=2143396

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

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/8845751

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The price of lost freedom: entropy of bimolecular complex formation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/8845751

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Trypsin-pancreatic trypsin inhibitor association. Dynamics of the interaction and role of disulfide bridges

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/8845751

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.5560050406

1 reference

10 October 2017

1 reference

10 October 2017

1 reference

PMCID

2143396