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Literature DB >> 14681393

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms.

Liam J McGuffin¹, Stefano A Street, Kevin Bryson, Søren-Aksel Sørensen, David T Jones.

Abstract

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

Entities: Chemical

Mesh：

Substances：
Proteins
Proteome

Year: 2004 PMID： 14681393 PMCID： PMC308777 DOI： 10.1093/nar/gkh043

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

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3. The GeneQuiz web server: protein functional analysis through the Web.

Authors: S Hoersch; C Leroy; N P Brown; M A Andrade; C Sander
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4. Structural characterization of the human proteome.

Authors: Arne Müller; Robert M MacCallum; Michael J E Sternberg
Journal: Genome Res Date: 2002-11 Impact factor: 9.043

5. 3D-Jury: a simple approach to improve protein structure predictions.

Authors: Krzysztof Ginalski; Arne Elofsson; Daniel Fischer; Leszek Rychlewski
Journal: Bioinformatics Date: 2003-05-22 Impact factor: 6.937

6. Gene3D: structural assignments for the biologist and bioinformaticist alike.

Authors: Daniel W A Buchan; Stuart C G Rison; James E Bray; David Lee; Frances Pearl; Janet M Thornton; Christine A Orengo
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

7. The PEDANT genome database.

Authors: Dmitrij Frishman; Martin Mokrejs; Denis Kosykh; Gabi Kastenmüller; Grigory Kolesov; Igor Zubrzycki; Christian Gruber; Birgitta Geier; Andreas Kaps; Kaj Albermann; Andreas Volz; Christian Wagner; Matthias Fellenberg; Klaus Heumann; Hans-Werner Mewes
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

8. Basic local alignment search tool.

Authors: S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

9. Improvement of the GenTHREADER method for genomic fold recognition.

Authors: Liam J McGuffin; David T Jones
Journal: Bioinformatics Date: 2003-05-01 Impact factor: 6.937

10. The distributed annotation system.

Authors: R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal: BMC Bioinformatics Date: 2001-10-10 Impact factor: 3.169

17 in total

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2. Protein superfamily evolution and the last universal common ancestor (LUCA).

Authors: Juan A G Ranea; Antonio Sillero; Janet M Thornton; Christine A Orengo
Journal: J Mol Evol Date: 2006-10-04 Impact factor: 2.395

Review 3. The proteome: structure, function and evolution.

Authors: Keiran Fleming; Lawrence A Kelley; Suhail A Islam; Robert M MacCallum; Arne Muller; Florencio Pazos; Michael J E Sternberg
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2006-03-29 Impact factor: 6.237

Review 4. Genome and proteome annotation: organization, interpretation and integration.

Authors: Gabrielle A Reeves; David Talavera; Janet M Thornton
Journal: J R Soc Interface Date: 2009-02-06 Impact factor: 4.118

5. Photox, a novel actin-targeting mono-ADP-ribosyltransferase from Photorhabdus luminescens.

Authors: Danielle D Visschedyk; Alexandru A Perieteanu; Zachari J Turgeon; Robert J Fieldhouse; John F Dawson; A Rod Merrill
Journal: J Biol Chem Date: 2010-02-24 Impact factor: 5.157

6. MYBBP1A: a new Ipr1's binding protein in mice.

Authors: Lei Cai; Hui Pan; Krzysztof Trzciński; Claudette M Thompson; Qiang Wu; Igor Kramnik
Journal: Mol Biol Rep Date: 2010-03-11 Impact factor: 2.316

7. Genome-wide Membrane Protein Structure Prediction.

Authors: Stefano Piccoli; Eda Suku; Marianna Garonzi; Alejandro Giorgetti
Journal: Curr Genomics Date: 2013-08 Impact factor: 2.236

8. HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

Authors: Charles Richard Bradshaw; Vineeth Surendranath; Robert Henschel; Matthias Stefan Mueller; Bianca Hermine Habermann
Journal: PLoS One Date: 2011-03-10 Impact factor: 3.240

9. Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

Authors: Bill Andreopoulos; Christof Winter; Dirk Labudde; Michael Schroeder
Journal: BMC Bioinformatics Date: 2009-06-27 Impact factor: 3.169

10. The ModFOLD4 server for the quality assessment of 3D protein models.

Authors: Liam J McGuffin; Maria T Buenavista; Daniel B Roche
Journal: Nucleic Acids Res Date: 2013-04-25 Impact factor: 16.971