Fast dynamics perturbation analysis for prediction of protein functional sites (Q33317416)

25 July 2017

title

Fast dynamics perturbation analysis for prediction of protein functional sites (English)

1 reference

25 July 2017

Judith D Cohn

0 references

Michael E Wall

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Dengming Ming

1 reference

25 July 2017

publication date

30 January 2008

1 reference

25 July 2017

published in

BMC Structural Biology

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25 July 2017

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25 July 2017

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A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites

25 July 2017

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21 June 2018

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ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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An evolutionary trace method defines binding surfaces common to protein families

21 June 2018

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21 June 2018

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21 June 2018

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Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

21 June 2018

1 reference

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Ligand binding and internal equilibiums in proteins

21 June 2018

1 reference

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Dynamics of carbon monoxide binding by heme proteins

21 June 2018

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Rate theories and puzzles of hemeprotein kinetics

21 June 2018

1 reference

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Structural origins of high-affinity biotin binding to streptavidin

21 June 2018

1 reference

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Crystal structure of an actinidin-E-64 complex

21 June 2018

1 reference

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Predicting and annotating catalytic residues: an information theoretic approach.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Travel depth, a new shape descriptor for macromolecules: application to ligand binding.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Interactions in native binding sites cause a large change in protein dynamics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

A method for localizing ligand binding pockets in protein structures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

An intuitive approach to measuring protein surface curvature.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Finding functional sites in structural genomics proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Using a neural network and spatial clustering to predict the location of active sites in enzymes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Distances and classification of amino acids for different protein secondary structures.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Automated construction of structural motifs for predicting functional sites on protein structures.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Relative entropy: free energy associated with equilibrium fluctuations and nonequilibrium deviations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Analysis of domain motions by approximate normal mode calculations

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Surface solid angle-based site points for molecular docking

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Network Analysis of Protein Structures Identifies Functional Residues

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2276503

Allostery in a coarse-grained model of protein dynamics

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18234095

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Automatic methods for predicting functionally important residues

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18234095

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dynamics of ligand binding to myoglobin

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18234095

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1472-6807-8-5

1 reference

Dimensions Publication ID

25 July 2017

0 references

1 reference

25 July 2017

1 reference