TOPDOM: database of domains and motifs with conservative location in transmembrane proteins

Summary: The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in α-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or mot...

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Autores principales: Tusnády, Gábor E., Kalmár, Lajos, Hegyi, Hédi, Tompa, Péter, Simon, István
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427164/
https://www.ncbi.nlm.nih.gov/pubmed/18434342
http://dx.doi.org/10.1093/bioinformatics/btn202
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author Tusnády, Gábor E.
Kalmár, Lajos
Hegyi, Hédi
Tompa, Péter
Simon, István
author_facet Tusnády, Gábor E.
Kalmár, Lajos
Hegyi, Hédi
Tompa, Péter
Simon, István
author_sort Tusnády, Gábor E.
collection PubMed
description Summary: The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in α-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy. Availability: The TOPDOM database and the constrained HMMTOP prediction server are available on the page http://topdom.enzim.hu Contact: tusi@enzim.hu; lkalmar@enzim.hu
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spelling pubmed-24271642009-02-25 TOPDOM: database of domains and motifs with conservative location in transmembrane proteins Tusnády, Gábor E. Kalmár, Lajos Hegyi, Hédi Tompa, Péter Simon, István Bioinformatics Applications Notes Summary: The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in α-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy. Availability: The TOPDOM database and the constrained HMMTOP prediction server are available on the page http://topdom.enzim.hu Contact: tusi@enzim.hu; lkalmar@enzim.hu Oxford University Press 2008-06-15 2008-04-23 /pmc/articles/PMC2427164/ /pubmed/18434342 http://dx.doi.org/10.1093/bioinformatics/btn202 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Tusnády, Gábor E.
Kalmár, Lajos
Hegyi, Hédi
Tompa, Péter
Simon, István
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title_full TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title_fullStr TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title_full_unstemmed TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title_short TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
title_sort topdom: database of domains and motifs with conservative location in transmembrane proteins
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427164/
https://www.ncbi.nlm.nih.gov/pubmed/18434342
http://dx.doi.org/10.1093/bioinformatics/btn202
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