SAHG
2016/05/09Web 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
- README
- Protein Basic Information
- Domain Modeling
- Complex Modeling
- Alignment
- Model Structure Thumbnail
- Domain Model Structure
- Complex Model Structure
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "SAHG" data. |
| File | README_e.html(English) |
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 item | Description |
|---|---|
| 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 |
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 item | Description |
|---|---|
| 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. |
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 item | Description |
|---|---|
| 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. |
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 item | Description |
|---|---|
| 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 |
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) |
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) |
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) |
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.
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:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- 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:
- 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.
- 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).
- 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
4. Update History
| Date | Update contents |
|---|---|
| 2016/05/09 | SAHG English archive site is opened. |
| 2009/10 | SAHG (http://bird.cbrc.jp/sahg) is opened. |
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 OtaSAHG, a comprehensive database of predicted structures of all human proteins
Nucleic Acids Research, 2011, Vol. 39,
PMID: 21051360
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