TMFunction

2017/01/23

Web Site: (Closed) http://tmbeta-genome.cbrc.jp/TMFunction/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/tmfunction/

TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. TMFunction data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "TMFunction" data.
File README_e.html (English)
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2.2 TMFunction data

Data name TMFunction data
Description of data contents TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the UniProt code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. are given in the database. Further, we have provided the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PubMed. In addition, complete reference is given with journal citation and PMID number.
File tmfunction.zip (48.5 KB)

Data items are the following:
Data itemDescription
Entry Entry
Residue(mutation) Name of residue with mutation
Residue Name of residue
Functionally important Functionally important or not
Function of the protein Function of the protein
Location Location of residue in the protein
Protein Name(abbreviation) Protein Name(abbreviation)
Source(scientific name) Source of protein (scientific name)
Source(english name) Source(english name)
Authors Authors of reference
Journal Reference Journal Reference
PMID PubMed ID of reference
Experiments Experiments
Experimental data The value with "Parameter" shows a measurement value in experiments.
Parameter Experimental parameter
Methods/conditions Experimental methods/conditions
PDB ID PDB ID of the protein structure
ASA Accessible surface area
Sec. Str Secondary structure of this protein
  • G: 3-10 helix
  • H: Helix
  • L: Loop
Uniprot ID UniProt ID of protein
Type Type of protein
Remarks Remarks
Keywords Keywords
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3. License

Last updated : 2017/01/23

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "TMFunction © Michael Gromiha (Indian Institute of Technology Madras) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Dr. M. MICHAEL GROMIHA
Associate Professor
Department of Biotechnology
IIT Madras
Chennai - 600 036
Tel: +91-44-2257-4138(O)
E-mail: gromiha[at]iitm[dot]ac[dot]in

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2017/01/23 TMFunction English archive site is opened.
2007/7 TMFunction (http://tmbeta-genome.cbrc.jp/TMFunction/) is opened.
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5. Literature

Gromiha MM, Yabuki Y, Suresh MX, Thangakani AM, Suwa M, Fukui K.
TMFunction: database for functional residues in membrane proteins.
Nucleic Acids Res. 2009 Jan;37(Database issue)
PMID: 18842639

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6. Contact address

When you have any question about "TMFunction", contact the following:

Dr. M. MICHAEL GROMIHA
Associate Professor
Department of Biotechnology
IIT Madras
Chennai - 600 036
Tel: +91-44-2257-4138(O)
E-mail: gromiha[at]iitm[dot]ac[dot]in

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