Prediction of protein-protein binding free energies (Q42201880)

18 October 2017

Prediction of protein-protein binding free energies (English)

1 reference

18 October 2017

1

Thom Vreven

1 reference

18 October 2017

Howook Hwang

2

1 reference

PMCID

3375440

18 October 2017

Brian G Pierce

series ordinal

3

1 reference

PMCID

3375440

18 October 2017

Zhiping Weng

series ordinal

4

1 reference

18 October 2017

2 February 2012

1 reference

18 October 2017

1 reference

18 October 2017

21

1 reference

18 October 2017

3

1 reference

18 October 2017

396-404

1 reference

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Integrating atom-based and residue-based scoring functions for protein-protein docking

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

A structure-based benchmark for protein-protein binding affinity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Protein-protein docking benchmark version 4.0.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Toward a quantitative theory of intrinsically disordered proteins and their function

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Electrostatic properties of protein-protein complexes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Intrinsically unstructured proteins and their functions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Effective energy functions for protein structure prediction.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Protein binding versus protein folding: the role of hydrophilic bridges in protein associations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

SCOP: a structural classification of proteins database for the investigation of sequences and structures

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Calculation of the free energy of association for protein complexes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Integrating statistical pair potentials into protein complex prediction.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

A novel empirical free energy function that explains and predicts protein-protein binding affinities.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Determination of atomic desolvation energies from the structures of crystallized 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=3375440

Protein-protein binding affinity prediction on a diverse set of structures

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Predicting kinetic constants of protein-protein interactions based on structural properties.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Multiple protonation equilibria in electrostatics of protein-protein binding

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Empirical parameters for estimating protein-protein binding energies: number of short- and long-distance atom-atom contacts.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

ZRANK: reranking protein docking predictions with an optimized energy function.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Optimal design of protein docking potentials: efficiency and limitations

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

ZDOCK: an initial-stage protein-docking algorithm.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

ZDOCK predictions for the CAPRI challenge.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375440

Are Scoring Functions in Protein−Protein Docking Ready to Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

17 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.2027

pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.2027

Protein-protein binding is often associated with changes in protonation state

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPRO.2027

Potential of mean force for protein-protein interaction studies

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22238219

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A fast empirical approach to binding free energy calculations based on protein interface information

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22238219

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/22238219

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.2027

1 reference

18 October 2017

1 reference

18 October 2017

1 reference

PMCID

3375440