Automated identification of functional dynamic contact networks from X-ray crystallography (Q27679361)

2

0 references

James S Fraser

object named as

James S Fraser

5

0 references

Peter Wright

object named as

Peter E Wright

4

0 references

author name string

Kun Yang

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

3

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publication date

September 2013

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published in

Nature Methods

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volume

10

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issue

9

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page(s)

896-902

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cites work

1 reference

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Accessing protein conformational ensembles using room-temperature X-ray crystallography

20 March 2017

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A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis

20 March 2017

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Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

20 March 2017

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Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

20 March 2017

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Structural and Energetic Mechanisms of Cooperative Autoinhibition and Activation of Vav1

20 March 2017

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PHENIX: a comprehensive Python-based system for macromolecular structure solution

20 March 2017

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Hidden alternative structures of proline isomerase essential for catalysis

20 March 2017

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Ensemble Refinement of Protein Crystal Structures: Validation and Application

20 March 2017

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The 1.0 A crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity

20 March 2017

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Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence

20 March 2017

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20 March 2017

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Phasercrystallographic software

20 March 2017

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Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

20 March 2017

1 reference

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Protein sectors: evolutionary units of three-dimensional structure

20 March 2017

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Molecular dynamics and protein function

20 March 2017

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Structure and dynamics of the G121V dihydrofolate reductase mutant: lessons from a transition-state inhibitor complex

20 March 2017

1 reference

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

20 March 2017

1 reference

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The dynamic energy landscape of dihydrofolate reductase catalysis

20 March 2017

1 reference

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Intrinsic dynamics of an enzyme underlies catalysis

7 April 2017

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7 April 2017

Decision making in xia2.

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A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase

29 September 2017

1 reference

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Modelling dynamics in protein crystal structures by ensemble refinement

29 September 2017

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Biomolecular simulation: a computational microscope for molecular biology

29 September 2017

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Mining electron density for functionally relevant protein polysterism in crystal structures

29 September 2017

1 reference

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Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

29 September 2017

1 reference

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Automated electron-density sampling reveals widespread conformational polymorphism in proteins

29 September 2017

1 reference

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The role of conformational entropy in molecular recognition by calmodulin

29 September 2017

1 reference

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Observing biological dynamics at atomic resolution using NMR.

29 September 2017

1 reference

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Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

29 September 2017

1 reference

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Computation of conformational coupling in allosteric proteins

29 September 2017

1 reference

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Characterizing and controlling the inherent dynamics of cyclophilin-A.

29 September 2017

1 reference

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Allosteric regulation and catalysis emerge via a common route.

29 September 2017

1 reference

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Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

29 September 2017

1 reference

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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

29 September 2017

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Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins

29 September 2017

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Simultaneous determination of protein structure and dynamics.

29 September 2017

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Biomolecular cryocrystallography: structural changes during flash-cooling

29 September 2017

1 reference

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The role of dynamics in allosteric regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760795

29 September 2017

1 reference

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Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism

29 September 2017

1 reference

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760795

Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760795

1H, 15N and 13C resonance assignments, secondary structure, and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760795

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

2 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.2592

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.2592

Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.2592

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.2592

1 reference

Dimensions Publication ID

576940

1035803529

0 references

576940

1 reference

1 reference

1 reference