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...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2008
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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 |
format | Text |
id | pubmed-2427164 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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