(Q33281571)

25 July 2017

title

Selective prediction of interaction sites in protein structures with THEMATICS. (English)

1 reference

protein structure prediction

25 July 2017

main subject

0 references

Mary Jo Ondrechen

4

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author name string

Ying Wei

series ordinal

1

1 reference

25 July 2017

Jaeju Ko

series ordinal

2

1 reference

25 July 2017

Leonel F Murga

series ordinal

3

1 reference

25 July 2017

publication date

9 April 2007

1 reference

25 July 2017

1 reference

25 July 2017

volume

8

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25 July 2017

page(s)

119

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Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.

25 July 2017

cites work

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21 June 2018

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21 June 2018

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Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves

21 June 2018

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Prediction of functional sites in proteins using conserved functional group analysis.

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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Future directions in protein function prediction.

21 June 2018

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THEMATICS: a simple computational predictor of enzyme function from structure

21 June 2018

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Prediction of functionally important residues based solely on the computed energetics of protein structure.

21 June 2018

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Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

21 June 2018

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21 June 2018

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Determination of protein function, evolution and interactions by structural genomics.

21 June 2018

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Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy

21 June 2018

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Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?

21 June 2018

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Computational genetics: finding protein function by nonhomology methods.

21 June 2018

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Mirroring perfection: the structure of methylglyoxal synthase complexed with the competitive inhibitor 2-phosphoglycolate

21 June 2018

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Biological function made crystal clear - annotation of hypothetical proteins via structural genomics

21 June 2018

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From genes to protein structure and function: novel applications of computational approaches in the genomic era.

21 June 2018

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21 June 2018

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Structural genomics: beyond the human genome project

21 June 2018

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Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily

21 June 2018

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Detecting protein function and protein-protein interactions from genome sequences

21 June 2018

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The crystal structure of methylglyoxal synthase from Escherichia coli

21 June 2018

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The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

21 June 2018

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Automated analysis of interatomic contacts in proteins

21 June 2018

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Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase

21 June 2018

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Class-directed structure determination: foundation for a protein structure initiative

21 June 2018

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Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases

21 June 2018

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Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+

21 June 2018

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Locating and characterizing binding sites on proteins

21 June 2018

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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

21 June 2018

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TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

21 June 2018

1 reference

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Structure-based analysis of catalysis and substrate definition in the HIT protein family

21 June 2018

1 reference

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Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Protein clefts in molecular recognition and function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

An evolutionary trace method defines binding surfaces common to protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Environmental effects on the protonation states of active site residues in bacteriorhodopsin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-->QAQ-B, in the reaction center

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Prediction of active sites for protein structures from computed chemical properties.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Active site prediction for comparative model structures with thematics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

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=1877815

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Mutagenic studies on histidine 98 of methylglyoxal synthase: effects on mechanism and conformational change

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Identification of substrate binding sites in enzymes by computational solvent mapping.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

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=1877815

Analysis of catalytic residues in enzyme active 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=1877815

Completeness in structural genomics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Phylogenetic inference in protein superfamilies: analysis of SH2 domains

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

Shining a light on structural genomics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877815

The determinants of pKas 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=1877815

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=1877815

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

31 October 2018

1 reference

12 December 2020

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

12 December 2020

A simple algorithm for the calculation of multiple site titration curves

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins

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12 December 2020

Structural genomics: keystone for a Human Proteome Project

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-8-119

1 reference

25 July 2017

DBLP publication ID

journals/bmcbi/WeiKMO07

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

25 July 2017

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