(Q33947797)

30 July 2017

title

THEMATICS: a simple computational predictor of enzyme function from structure (English)

1 reference

30 July 2017

M J Ondrechen

1

1 reference

30 July 2017

J G Clifton

series ordinal

2

1 reference

30 July 2017

D Ringe

series ordinal

3

1 reference

30 July 2017

language of work or name

English

0 references

publication date

16 October 2001

1 reference

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

30 July 2017

published in

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30 July 2017

volume

98

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30 July 2017

issue

22

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30 July 2017

page(s)

12473-12478

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

30 July 2017

cites work

1 reference

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Mining the draft human genome

5 July 2018

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

5 July 2018

1 reference

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5 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Identification of protein coding regions by database similarity search

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Tyrosine-48 is the proton donor and histidine-110 directs substrate stereochemical selectivity in the reduction reaction of human aldose reductase: enzyme kinetics and crystal structure of the Y48H mutant enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

An anion binding site in human aldose reductase: mechanistic implications for the binding of citrate, cacodylate, and glucose 6-phosphate

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Identification of Site in Triose Phosphate Isomerase Labelled by Glycidol Phosphate

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

A model for enzyme-substrate interaction in alanine racemase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Arginine 304 Is an Active Site Residue in Phosphomannose Isomerase from Candida albicans

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Using meta computing tools to facilitate large-scale analyses of biological databases.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Studies on phosphomannose isomerase. I. Isolation, homogeneity measurements, and determination of some physical properties

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=60078

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

29 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

On the calculation of pKas in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Uniquely Labelled Active Site Sequence in Chicken Muscle Triose Phosphate Isomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Partial sequence of an active-site peptide from triose phosphate isomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates; comparison with phosphomannoisomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.211436698

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11606719

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.211436698

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference