Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites (Q34323850)

1 August 2017

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites (English)

1 reference

1 August 2017

0 references

Gregory R Bowman

1

1 reference

PubMed ID

22753506

1 August 2017

Phillip L Geissler

series ordinal

2

1 reference

PubMed ID

22753506

1 August 2017

language of work or name

English

0 references

publication date

2 July 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

1 August 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

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1 August 2017

109

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1 August 2017

29

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1 August 2017

11681-11686

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Novel allosteric sites on Ras for lead generation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

The role of protein conformational fluctuations in allostery, function, and evolution.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

An allosteric inhibitor of the human Cdc34 ubiquitin-conjugating enzyme

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

A role for both conformational selection and induced fit in ligand binding by the LAO protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Turning a protein kinase on or off from a single allosteric site via disulfide trapping

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome P450 CYP119.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

The hidden energetics of ligand binding and activation in a glutamate receptor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Mechanisms of protein-ligand association and its modulation by protein mutations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Modeling conformational ensembles of slow functional motions in Pin1-WW

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Protein folded states are kinetic hubs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Network models for molecular kinetics and their initial applications to human health

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Conformational selection or induced fit: a flux description of reaction mechanism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Using generalized ensemble simulations and Markov state models to identify conformational states

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Probing the flexibility of large conformational changes in protein structures through local perturbations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Transition networks for modeling the kinetics of conformational change in macromolecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Enzyme adaptation to inhibitor binding: a cryptic binding site in phenylethanolamine N-methyltransferase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

COMPUTING: Screen Savers of the World Unite!

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Exploitation of structural and regulatory diversity in glutamate racemases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Searching for new allosteric sites in enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Discovery of a novel binding trench in HIV integrase.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Binding of small molecules to an adaptive protein-protein interface

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Site-directed ligand discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Evolutionarily conserved pathways of energetic connectivity in protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406870

Allosteric inhibition through core disruption.

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Biochemistry. An ensemble view of allostery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Computational approach to site-directed ligand discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Conformational selection versus induced fit in kinases: the case of PI3K-γ.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Structural and mutational studies of organophosphorus hydrolase reveal a cryptic and functional allosteric-binding site

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1209309109

Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22753506

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1209309109

1 reference

1 August 2017

0 references

1 reference

1 August 2017

1 reference

PubMed ID

22753506