GRIPDB

2017/07/19

Web Site: (Closed) http://grip.cbrc.jp/GDB/index.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/gripdb/

The database provides information about GPCR oligomerization.

README Content

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

1. Database Component

  1. README
  2. GPCR Interaction
  3. Experiment information
  4. GPCR Mutation information
  5. Prediction information
  6. GPCR sequence information
  7. GRIP Database original data
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2. Data Description

2.1 README

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

Data name GPCR Interaction
Description of data contents

This is the list of GPCR (G protein-coupled receptor) interacting and related information (disease etc.).
File gripdb_main.zip (25.4 KB)

Data items are the following:
Data itemDescription
GRIP ID Interaction ID
Main Title Interaction title
GPCR Class GPCR Class
GPCR Subfamily GPCR Subfamily
GPCR Subtype GPCR Subtype
GPCR Name GPCR Name
Partner Class Partner Class
Partner Subfamily Partner Subfamily
Partner Subtype Partner Subtype
Partner Name Partner Name
Evidence Kind of evidence
"Experiment" or "Prediction"
Annotations Annotations of the interaction
Articles Reference article (PubMed ID)
Methods Methods of the evidence
Target Sequence ID of the GPCR
Other Partners Other partners than "Patner Name"
Disease Disease information related with the interaction
Interface GPCR interface
Mutation Information Link to GPCR mutation information (simple search only)
Experiment Information Link to experiment information (simple search only)
Predicted Information Link to predicted information (simple search only)
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2.3 Experiment information

Data name Experiment information
Description of data contents

Experimentally identified GPCR interaction regions
File gripdb_exp_info.zip (6.2 KB)

Data items are the following:
Data itemDescription
ID Experiment information ID
GRIP ID1 GRIP ID related wigh the experiment
GRIP ID2 No. in GRIP ID1
Template Reference template of GRIP ID1's interface
Target Sequence ID of the GPCR
Interface Interface of GRIP ID1
Template Start Start sequence position of the interface in reference template
Template End End sequence position of the interface in reference template
Target Start Start sequence position of the interface in GRIP ID1
Target End End sequence position of the interface in GRIP ID1
Annotation Annotation
Article Reference article (PubMed ID)
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2.4 GPCR Mutation information

Data name GPCR Mutation information
Description of data contents

GPCR sequence mutations which are confirmed in experiments and exposed in molecular surface.
File gripdb_mutation_info.zip (766 bytes)

Data items are the following:
Data itemDescription
ID Mutation information ID
GPCR GPCR Name
Mutation Type Mutation type
Template Reference template
Target GPCR sequence ID
Template Start Corresponding sequence start position in the reference template
Template End Corresponding sequence end position in the reference template
Target Start Mutation start position in the GPCR
Target End Mutation end position in the GPCR
Variation Variation of the mutation
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2.5 Prediction information

Data name Prediction information
Description of data contents

Predicted GPCR interaction regions
File gripdb_predicted_info.zip (219 KB)

Data items are the following:
Data itemDescription
ID Prediction information ID
GRIP ID GRIP ID related wigh the prediction
Prediction No Prediction No. (Sequential No. in GRIP ID)
Template Reference template of GRIP ID's interface
Target Sequence ID of the GPCR
Template Pos Start sequence position of the interface in reference template
Template Seq End sequence position of the interface in reference template
Target Pos Start sequence position of the interface in GRIP ID
Target Seq End sequence position of the interface in GRIP ID
CONS(i) Conservativation
Article Reference article (PubMed ID)
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2.6 GPCR sequence information

Data name GPCR sequence information
Description of data contents

GPCR sequence information
File gripdb_seq.zip (258 KB)

Data items are the following:
Data itemDescription
Sequence ID Sequence ID
Sequence Sequence
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2.7 GRIP Database original data

Data name GRIP Database original data
Description of data contents

GRIP Database original data
It consists of data tables and sequences.
File gripdb_original_data.zip (779 KB)
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3. License

Last updated : 2017/07/19

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: "GRIPDB © Wataru Nemoto (National Institute of Advanced Industrial Science and Technology) 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.

Wataru Nemoto
E-mail : w[dot]nemoto[at]mail[dot]dendai[dot]ac[dot]jp

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4. Update History

DateUpdate contents
2017/07/19 GRIPDB English archive site is opened.
2009/01/30 GRIPDB (http://grip.cbrc.jp/GDB/index.html) is opened.
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5. Literature

Nemoto W, Fukui K, Toh H.
GRIPDB - G protein coupled Receptor Interaction Partners DataBase.
J Recept Signal Transduct Res. 2011 Jun;31(3):199-205.
PMID: 21410407

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6. Contact address

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

Wataru Nemoto

E-mail : w[dot]nemoto[at]mail[dot]dendai[dot]ac[dot]jp

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