(Q35164244)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

title

Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

4

Anna R Panchenko

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

author name string

Marharyta Petukh

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Emil Alexov

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

publication date

27 February 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

17 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

page(s)

1770-1780

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

All-atom empirical potential for molecular modeling and dynamics studies of proteins

17 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Molecular origins of binding affinity: seeking the Archimedean point

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Cancer missense mutations alter binding properties of proteins and their interaction networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Impact of mutations on the allosteric conformational equilibrium

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Predicting folding free energy changes upon single point mutations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Parallel Generalized Born Implicit Solvent Calculations with NAMD.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Relative solvent accessible surface area predicts protein conformational changes upon binding

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Triathlon for energy functions: who is the winner for design of protein-protein interactions?

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Computational analysis of missense mutations causing Snyder-Robinson syndrome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Modeling effects of human single nucleotide polymorphisms on protein-protein interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Solvent dramatically affects protein structure refinement.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

A new generation of statistical potentials for proteins.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Scalable molecular dynamics with NAMD

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Prediction of water and metal binding sites and their affinities by using the Fold-X force field

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

The modular architecture of protein-protein binding interfaces

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Exploring the origins of binding specificity through the computational redesign of calmodulin

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Computational alanine scanning of the 1:1 human growth hormone-receptor complex

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

13 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Canonical dynamics: Equilibrium phase-space distributions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Influence of the membrane potential on the free energy of an intrinsic protein

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Automated design of the surface positions of protein helices

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

VMD: visual molecular dynamics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Electrostatic interactions in macromolecules: theory and applications

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Principles of protein-protein recognition

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

pH-selective mutagenesis of protein-protein interfaces: in silico design of therapeutic antibodies with prolonged half-life

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

A simple definition of structural regions in proteins and its use in analyzing interface evolution.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Computational design of peptides that target transmembrane helices.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

The physics and bioinformatics of binding and folding-an energy landscape perspective

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Structural characterisation and functional significance of transient protein-protein interactions

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Modeling implicit reorganization in continuum descriptions of protein-protein interactions

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

The dielectric constant of a folded protein

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Unraveling the Importance of Protein−Protein Interaction: Application of a Computational Alanine-Scanning Mutagenesis to the Study of the IgG1 Streptococcal Protein G (C2 Fragment) Complex

16 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985714

Validation and use of the MM-PBSA approach for drug discovery

16 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24803870

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting free energy changes using structural ensembles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24803870

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT401022C

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803870%20AND%20SRC:MED&resulttype=core&format=json