SAHG

2016/05/09

Web Site: http://bird.cbrc.jp/sahg
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/sahg/

SAHG is a comprehensive database of predicted structures of all human 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. Protein Basic Information
  3. Domain Modeling
  4. Complex Modeling
  5. Alignment
  6. Model Structure Thumbnail
  7. Domain Model Structure
  8. Complex Model Structure
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2. Data Description

2.1 README

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

Data name Protein Basic Information
Description of data contents Basic information of the target protein. Amino acid sequence, RefSeq ID, etc.
File sahg_protein.zip (8.1 MB)

Data items are the following:
Data itemDescription
RefSeqID RefSeq ID
domainSize Number of linked Domain Modeling
Link to Domain (only in SimpleSearch pages) link to Domain Modeling of the same RefSeqID
Link to Complex (only in SimpleSearch pages) link to Complex Modeling of the same RefSeqID
GeneID Entrez Gene ID of the gene coding the protein
Definition Protein name in RefSeq database
chromosome Chromosome number of the gene
Location Locus of the gene
Sequence Amino acid sequence
EC number Enzyme Commission numbers
EzCatDB EzCatDB (A Database of Enzyme Catalytic Mechanisms) ID
HPRD Human Protein Reference Database (HPRD) ID
Swiss-Prot (only in SimpleSearch pages) link to UniProtKB/Swiss-Prot
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2.3 Domain Modeling

Data name Domain Modeling
Description of data contents Predicted structure of the domain, information of the templates, predicted interactions.
File sahg_domain.zip (3.4 MB)

Data items are the following:
Data itemDescription
RefSeqID RefSeq ID
Link to Protein (only in SimpleSearch pages) link to Protein Basic Information of the same RefSeqID
chromosome Chromosome number of the gene
domainIdx Domain index (sequential) for a protein
apoholoNum 1: Only apo form was modeled. 2:Only holo form. 3:Both apo and holo forms
aafrom Starting amino acid residue number.
aato Ending amino acid residue number.
Domain description Function of the domain region (predicted based on the template protein information).
apo Template Template protein in apo form.
apo model PDB Link to the predicted structure.
holo Template Template protein in holo form.
holo model PDB Link to the predicted structure.
Detected by Template search methods
Ligand Binding Residues Ligand binding residues
Interface Residues Protein-protein interaction residues
Catalytic Residues Catalytic residues (only for enzymes)
Ligand PDBchemical ID for the predicted ligands
morphing 0: No animation data. 1: animation data presented.
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2.4 Complex Modeling

Data name Complex Modeling
Description of data contents Protein-protein copmlex modeling predition
File sahg_complex.zip (147 KB)

Data items are the following:
Data itemDescription
RefSeqID RefSeq ID
Link to Protein (only in SimpleSearch pages) link to Protein Basic Information of the same RefSeqID
regionFrom Starting amino acid residue number.
regionTo Ending amino acid residue number.
model PDB (only in SimpleSearch pages) link to model structure (PDB)
Oligomer homo oligomer / hetero oligomer
Model Model index (sequential) for a protein
Template Template for the complex modeling
Partner ID RefSeq ID of the counterpart protein in the complex.
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2.5 Alignment

Data name Alignment
Description of data contents Alignment between target and template sequences
File sahg_alignment.zip (12.0 MB)

Data items are the following:
Data itemDescription
RefSeqID RefSeq ID
Domain_type Type of domain structure (apo or holo)
Template Template protein name
Query_from Starting amino acid residue number of the aligned region of the target protein.
Query_to Ending amino acid residue number of the aligned region of the target protein.
Query_alignment Alignment sequence (query)
Template_from Starting amino acid residue number of the aligned region of the template protein.
Template_to Ending amino acid residue number of the aligned region of the template protein.
Template_alignment Alignment sequence (template)
Alignment_line Line of alignment
Identity(%) Sequence identity
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2.6 Model Structure Thumbnail

Data name Model Structure Thumbnail
Description of data contents Still/animated images of the predicted protein domain sturctures.
File model_structure_thumbnail.zip (404 MB)
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2.7 Domain Model Structure

Data name Domain Model Structure
Description of data contents Predicted protein structure (PDB format).
File domain_model_structure.zip (1.6 GB)
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2.8 Complex Model Structure

Data name Complex Model Structure
Description of data contents Predicted protein compex structure (PDB format).
File complex_model_structure.zip (1.1 GB)
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3. License

Last updated : 2016/05/09

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: "SAHG © Motono Chie (The Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)) 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.

Chie Motono
Tel : +81-3-3599-8067
E-mail: c-motono[at]aist[dot]go[dot]jp

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4. Update History

DateUpdate contents
2016/05/09 SAHG English archive site is opened.
2009/10 SAHG (http://bird.cbrc.jp/sahg) is opened.
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5. Literature

Chie Motono, Junichi Nakata, Ryotaro Koike, Kana Shimizu, Matsuyuki Shirota, Takayuki Amemiya, Kentaro Tomii, Nozomi Nagano, Naofumi Sakaya, Kiyotaka Misoo, Miwa Sato, Akinori Kidera, Hidekazu Hiroaki, Tsuyoshi Shirai, Kengo Kinoshita, Tamotsu Noguchi, Motonori Ota
SAHG, a comprehensive database of predicted structures of all human proteins
Nucleic Acids Research, 2011, Vol. 39,
PMID: 21051360

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6. Contact address

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

Chie Motono
Tel : +81-3-3599-8067
E-mail: c-motono[at]aist[dot]go[dot]jp

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