(Q24647889)

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

inferred from page(s)

published in

Biophysical Journal

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volume

96

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issue

12

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page(s)

4993-5002

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cites work

1 reference

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HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

7 April 2017

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Inhibitor binding studies on enoyl reductase reveal conformational changes related to substrate recognition

7 April 2017

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Structure and function of the multifunctional DNA-repair enzyme exonuclease III

7 April 2017

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Optimal description of a protein structure in terms of multiple groups undergoing TLS motion

7 April 2017

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HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

7 April 2017

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Proteases universally recognize beta strands in their active sites

7 April 2017

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How enzymes work: analysis by modern rate theory and computer simulations

7 April 2017

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The universal protein resource (UniProt)

7 April 2017

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The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

7 April 2017

1 reference

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Essential dynamics of proteins

7 April 2017

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The Energy Landscapes and Motions of Proteins

7 April 2017

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Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics

7 April 2017

1 reference

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Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments

28 September 2017

1 reference

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Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways

28 September 2017

1 reference

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Atomistic simulations of the HIV-1 protease folding inhibition

28 September 2017

1 reference

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CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

28 September 2017

1 reference

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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

28 September 2017

1 reference

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Illuminating the mechanistic roles of enzyme conformational dynamics

28 September 2017

1 reference

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Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages

28 September 2017

1 reference

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A natural coarse graining for simulating large biomolecular motion

28 September 2017

1 reference

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Folding and binding cascades: dynamic landscapes and population shifts

28 September 2017

1 reference

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Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Molecular dynamics of apo-adenylate kinase: a principal component analysis

30 May 2018

1 reference

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Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

30 May 2018

1 reference

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Enzymology. A moving story

30 May 2018

1 reference

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Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations.

30 May 2018

1 reference

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Conformational diversity of ligands bound to proteins

30 May 2018

1 reference

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Hierarchical clustering of the correlation patterns: new method of domain identification in proteins.

28 November 2018

1 reference

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Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

28 November 2018

1 reference

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Automatic domain decomposition of proteins by a Gaussian Network Model.

28 November 2018

1 reference

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Structural basis for the variation in triclosan affinity to enoyl reductases

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

DNA binding provides a molecular strap activating the adenovirus proteinase

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Analysis of domain motions by approximate normal mode calculations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712024

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

28 November 2018

1 reference

12 December 2020

Analysis of domain motions in large proteins

1 reference

12 December 2020

Superparamagnetic clustering of data

1 reference

12 December 2020

Convergent dynamics in the protease enzymatic superfamily

1 reference

12 December 2020

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps

1 reference

12 December 2020

10.1016/J.BPJ.2009.03.051

Identifiers

DOI

1 reference

1 reference

1 reference

PubMed publication ID

19527659

1 reference