DB-SPIRE

2017/02/16

Web Site: (Closed) http://mbs.cbrc.jp/DB-SPIRE
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/dbspire/

This database has the positional information in the amino acid motif structure. The information is identified by experiments or sequence analysis.

README Content

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

1. Database Component

  1. README
  2. PROSITE List
  3. PROSITE Information
  4. PROSITE - PDB SEQRES matching
  5. BLOCKS List
  6. BLOCKS Information
  7. BLOCKS - PDB matching
  8. BLOCKS - PDB SEQRES matching
  9. BLOCKS - PDB ATOM matching
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "DB-SPIRE" data.
File README_e.html (English)
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2.2 PROSITE List

Data name PROSITE List
Description of data contents

The list shows PROSITE entries and PDB entry/chain matching status.
File dbspire_prosite_list.zip (29.1 KB)

Data items are the following:
Data itemDescription
prositeLisAC PROSITE DO
PROSITE Info Link to PROSITE Information from prositeLisAC (simple search only)
prositeLisFamilySize Number of ACs for this PROSITE DO
prositeLisDE Description of this PROSITE DO
prositeLisPatternSize Number of "Pattern" ACs for this PROSITE DO
prositeLisRuleSize Number of "Rule" ACs for this PROSITE DO
prositeLisRuleWithPASize Number of "Pattern" and "Rule" ACs for this PROSITE DO
prositeLisRuleWithMASize Number of "Matrix" and "Rule" ACs for this PROSITE DO
prositeLisMatrixSize Number of "Matrix" ACs for this PROSITE DO
prosite3dLisIdSize Number of PDB entries for this PROSITE DO (in PROSITE)
prosite3dSeqIdLisSize Number of PDB entries whose SEQRES matches this PROSITE DO
prosite3dSeqChainLisSize Number of PDB chains whose SEQRES matches this PROSITE DO
prosite3dAtomIdLisSize Number of PDB entries whose ATOM matches this PROSITE DO
prosite3dAtomChainLisSize Number of PDB chains whose ATOM matches this PROSITE DO
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2.3 PROSITE Information

Data name PROSITE Information
Description of data contents

It shows PROSITE entries and PDB entry/chain matching status.
File dbspire_prosite_info.zip (54.8 KB)

Data items are the following:
Data itemDescription
prositeAC PROSITE Accession
PDB SEQRES Link to PROSITE - PDB SEQRES matching from prositeAC (simple search only)
prositeID PROSITE ID
prositeIDType Accession type
prositeDE Description of this entry
prositeDO PROSITE DO of this entry
prosite3dSize Number of PDB entries for this entry (in PROSITE)
prosite3dSeqIdSize Number of PDB entries whose SEQRES matches this entry
prosite3dSeqChainSize Number of PDB chains whose SEQRES matches this entry
prosite3dAtomIdSize Number of PDB entries whose ATOM matches this entry
prosite3dAtomChainSize Number of PDB chains whose ATOM matches this entry
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2.4 PROSITE - PDB SEQRES matching

Data name PROSITE - PDB SEQRES matching
Description of data contents

Sequence numbers of PDB entries/chains whose SEQRES matches a PROSITE entry
File dbspire_prosite_pdb_seq.zip (4.1 MB)

Data items are the following:
Data itemDescription
prositeAC PROSITE Accession
pdbID PDB ID
pdbChain PDB chain
pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this PROSITE entry
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2.5 BLOCKS List

Data name BLOCKS List
Description of data contents

The list shows BLOCKS entries and PDB entry/chain matching status.
File dbspire_blocks_list.zip (113 KB)

Data items are the following:
Data itemDescription
blocksFamilyAC BLOCKS Family Accession
BLOCKS Info Link to BLOCKS Information from blocksFamilyAC (simple search only)
blocksType Origing of this entry (PRINTS or PROTMAT)
blocksFamilySize Number of ACs for this family accession
blocksPrints PRINTS Accession (only from PRINTS)
blocksName Description of this entry
blocks3dIdFamilySize Number of PDB entries annotated with this entry by MAST
blocks3dChainFamilySize Number of PDB chains annotated with this entry by MAST
blocks3dSeqIdFamilySize Number of PDB entries whose SEQRES matches this entry
blocks3dSeqChainFamilySize Number of PDB chains whose SEQRES matches this entry
blocks3dAtomIdFamilySize Number of PDB entries whose ATOM matches this entry
blocks3dAtomChainFamilySize Number of PDB chains whose ATOM matches this entry
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2.6 BLOCKS Information

Data name BLOCKS Information
Description of data contents

It shows BLOCKS entries and PDB entry/chain matching status.
File dbspire_blocks_info.zip (305 KB)

Data items are the following:
Data itemDescription
blocksAC BLOCKS Accession
PDB SEQRES Link to BLOCKS - PDB SEQRES matching from BLOCKS AC (simple search only)
PDB ATOM Link to BLOCKS - PDB ATOM matching from BLOCKS AC (simple search only)
blocksACFamily BLOCKS Family Accession
Family VS PDB Link to BLOCKS - matching from BLOCKS AC Family (simple search only)
blocksID BLOCKS ID
blocksDE Description of this entry
blocks3dIdSize Number of PDB entries annotated with this entry by MAST
blocks3dChainSize Number of PDB chains annotated with this entry by MAST
blocks3dSeqIdSize Number of PDB entries whose SEQRES matches this entry
blocks3dSeqChainSize Number of PDB chains whose SEQRES matches this entry
blocks3dAtomIdSize Number of PDB entries whose ATOM matches this entry
blocks3dAtomChainSize Number of PDB chains whose ATOM matches this entry
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2.7 BLOCKS - PDB matching

Data name BLOCKS - PDB matching
Description of data contents

PDB entries/chains which matches a BLOCKS entry
File dbspire_blocks_pdb.zip (512 KB)

Data items are the following:
Data itemDescription
blocksFamilyAC BLOCKS Family Accession
pdbID PDB ID
pdbChain PDB Chain
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2.8 BLOCKS - PDB SEQRES matching

Data name BLOCKS - PDB SEQRES matching
Description of data contents

Sequence numbers of PDB entries/chains whose SEQRES matches a BLOCKS entry
File dbspire_blocks_pdb_seq.zip (6.4 MB)

Data items are the following:
Data itemDescription
blocksFamilyAC BLOCKS Accession
pdbID PDB ID
pdbChain PDB Chain
pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this BLOCKS entry
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2.9 BLOCKS - PDB ATOM matching

Data name BLOCKS - PDB ATOM matching
Description of data contents

Sequence numbers of PDB entries/chains whose ATOM matches a BLOCKS entry
File dbspire_blocks_pdb_atom.zip (6.2 MB)

Data items are the following:
Data itemDescription
blocksFamilyAC BLOCKS Accession
pdbID PDB ID
pdbChain PDB Chain
pdbIndex ATOM Start position
pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this BLOCKS entry
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3. License

Last updated : 2017/02/16

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: "DB-SPIRE © Tamotsu Noguchi (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.

Tamotsu Noguchi
Tel: 042-495-8736
E mail: noguchit[at]my-pharm[dot]ac[dot]jp

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
2017/02/16 DB-SPIRE English archive site is opened.
2005/04/01 DB-SPIRE (http://mbs.cbrc.jp/DB-SPIRE) is opened.
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5. Literature

-
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6. Contact address

When you have any question about "DB-SPIRE", contact the following:

Tamotsu Noguchi
Tel: 042-495-8736
E mail: noguchit[at]my-pharm[dot]ac[dot]jp

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