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Protocols

TMPDB specifications

Information


Unique identifier OMICS_30169
Name TMPDB
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained No

Publication for TMPDB

TMPDB citations

 (5)
library_books

Development of a Machine Learning Method to Predict Membrane Protein Ligand Binding Residues Using Basic Sequence Information

2015
Adv Bioinformatics
PMCID: 4329842
PMID: 25802517
DOI: 10.1155/2015/843030

[…] brane proteins was extracted from structures of known membrane protein-ligand complexes in the Protein Data Bank []. The dataset was culled using the list of membrane proteins obtained from PDBTM [], TMPDB [], MPDB [], and a large collection of membrane protein structures []. The resulting dataset consists of 31 membrane proteins from which 42 sequences (nonhomologous chains are taken into account […]

library_books

Annotation of protein residues based on a literature analysis: cross validation against UniProtKb

2009
BMC Bioinformatics
PMCID: 2745586
PMID: 19758468
DOI: 10.1186/1471-2105-10-S8-S4

[…] ting information from biomedical articles in the view of updating existing databases. For example, scientific articles have been used to generate the specialised databases DOLOP (lipoprotein) [], and TMPDB (transmembrane proteins) []. Clearly, annotations can be used to verify data mined sequence or structure patterns and likewise an identified pattern provides a context to interpret functional an […]

library_books

IgTM: An algorithm to predict transmembrane domains and topology in proteins

2008
BMC Bioinformatics
PMCID: 2566583
PMID: 18783592
DOI: 10.1186/1471-2105-9-367

[…] 08 multi-spanning and 52 single-spanning proteins. The original dataset was larger, but those proteins whith conflicting topologies for different experiments were not included.The second set used was TMPDB [], whose latest version (Release 6.3) contains 302 transmembrane protein sequences (276 alpha-helical sequences, 17 beta-stranded sequences and 9 alpha-helical sequences with short pore-forming […]

library_books

Evaluating eukaryotic secreted protein prediction

2005
BMC Bioinformatics
PMCID: 1276785
PMID: 16225690
DOI: 10.1186/1471-2105-6-256

[…] ansmembrane domains and is designed to differentiate N-terminal transmembrane domains from CTT signal peptides. The HMMs were trained using 146 sequences from the TMHMM dataset [], 140 sequences from TMPDB [], 2 sequences from the Moller dataset [], and 4 TM sequences from SWISS-PROT. These sequences were divided into TM-only and TM-and-SP sequence sets. Additionally, SP-only and not-TM-not-SP seq […]

call_split

Prediction of β barrel membrane proteins by searching for restricted domains

2005
BMC Bioinformatics
PMCID: 1280923
PMID: 16225682
DOI: 10.1186/1471-2105-6-254
call_split See protocol

[…] In order to evaluate the prediction, the following sequence pools were created with a redundancy of maximal 50%. From the TMPDB [] databank we retrieved the file TMPDB_alpha_nr_PR.dat [] which contains a set of α-helical transmembrane proteins. We further collected all OM proteins from the experimentally verified ePSortd […]

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TMPDB institution(s)
Department of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki, Japan; Science of Bioresources Program, The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
TMPDB funding source(s)
Supported in part by a Grant-in-Aid for Scientific Research on Priority Areas (C) ‘Genome Information Science’ from the Ministry of Education, Culture, Sports, Science and Technology of Japan (grant 14015203).

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