PoSSuM

2019/03/28

Web Site: http://possum.cbrc.jp/PoSSuM/index.html

A database for detecting similar small-molecule binding sites on 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. Known binding sites
  3. Potential binding sites
  4. Known binding site similarities
  5. Binding site similarities
  6. (Drug Search)Ligand list
  7. (Drug Search)Query site list
  8. (Drug Search)Target site list
  9. (Drug Search)Target ligand list
  10. (Drug Search)Known binding site similarity
  11. (Drug Search)Known binding site similarity
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2. Data Description

2.1 README

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

Data name Known binding sites
Description of data contents

Known binding sites on protein
File possum_ksite.zip (7.9 MB)

Data items are the following:
Data itemDescription
PocketIndex Internal ID for this binding site
PDB_ID PDB ID for the protein
HET_Code HET code for the ligand
ChainID ID for the chain where the binding site is
HET_Res.No. Residue sequence number of the ligand
ResLength Length of residue sequence of the site
Atoms Num of atoms of the ligand
MolName Molecular name of the site
EC EC ID for the site
CATH CATH ID for the site
SCOPe SCOPe ID for the site
UniProt UniProt ID for the site
UniRef50 UniRef50 cluster ID for the site (when it is analysed)
GO1 Gene ontology to indicate molecular function of the site
GO2 Gene ontology to indicate molecular function of the site
GO3 Gene ontology to indicate molecular function of the site
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2.3 Potential binding sites

Data name Potential binding sites
Description of data contents

Not confirmed yet but putative binding sites on protein
File possum_psite.zip (27 MB)

Data items are the following:
Data itemDescription
PocketIndex Internal ID for this binding site
PDB_ID PDB ID for the protein
HET_Code HET code for the ligand
ChainID ID for the chain where the binding site is
ResLength Length of residue sequence of the site
Atoms Num of atoms of the ligand
MolName Molecular name of the site
EC EC ID for the site
CATH CATH ID for the site
SCOPe SCOPe ID for the site
UniProt UniProt ID for the site
UniRef50 UniRef50 cluster ID for the site (when it is analysed)
GO1 Gene ontology to indicate molecular function of the site
GO2 Gene ontology to indicate molecular function of the site
GO3 Gene ontology to indicate molecular function of the site
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2.4 Known binding site similarities

Data name Known binding site similarities
Description of data contents

Similarity data between known binding sites
File possum_kpair.zip (3.9 GB)

Data items are the following:
Data itemDescription
Q:PocketIndex Internal ID for query site
Ｔ:PocketIndex Internal ID for target site
Q:PDB_ID PDB ID for query site
T:PDB_ID PDB ID for target site
Q:HET_Code HED code for query site
T:HET_Code HED code for target site
Q:ChainID ID for the chain where the query site is
T:ChainID ID for the chain where the target site is
Q:Res.No. Residence number for the amino acid where the query site is
T:Res.No. Residence number for the amino acid where the target site is
Cosine Cosine similarity with physicochemical and geometric properties
AlignedLength Length of amino acid alignment
RMSD Root Mean Square Deviation
TM-score Template modeling score of protein structure
Pval P-Value of similarity
AminoIdentity Amino acid match rate
MolName Molecular name of the site
EC EC ID for the site
CATH CATH ID for the site
SCOPe SCOPe ID for the site
UniProt UniProt ID for the site
UniRef50 UniRef50 cluster ID for the site (when it is analysed)
GO1 Gene ontology to indicate molecular function of the site
GO2 Gene ontology to indicate molecular function of the site
GO3 Gene ontology to indicate molecular function of the site
AlignedResidues Amino acid alignment result
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2.5 Binding site similarities

Data name Binding site similarities
Description of data contents

Similarity data between known/potential binding sites
File possum_ppair.zip (5.4 GB)

Data items are the following:
Data itemDescription
Q:PocketIndex Internal ID for query site
Ｔ:PocketIndex Internal ID for target site
Q:PDB_ID PDB ID for query site
T:PDB_ID PDB ID for target site
Q:HET_Code HED code for query site
T:HET_Code HED code for target site
Q:ChainID ID for the chain where the query site is
T:ChainID ID for the chain where the target site is
Q:Res.No. Residence number for the amino acid where the query site is
T:Res.No. Residence number for the amino acid where the target site is
Cosine Cosine similarity with physicochemical and geometric properties
AlignedLength Length of amino acid alignment
RMSD Root Mean Square Deviation
TM-score Template modeling score of protein structure
Pval P-Value of similarity
AminoIdentity Amino acid match rate
MolName Molecular name of the site
EC EC ID for the site
CATH CATH ID for the site
SCOPe SCOPe ID for the site
UniProt UniProt ID for the site
UniRef50 UniRef50 cluster ID for the site (when it is analysed)
GO1 Gene ontology to indicate molecular function of the site
GO2 Gene ontology to indicate molecular function of the site
GO3 Gene ontology to indicate molecular function of the site
AlignedResidues Amino acid alignment result
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2.6 (Drug Search)Ligand list

Data name (Drug Search)Ligand list
Description of data contents

Ligand list for Drug Search extracted from ChEMBL
File possum_ligand_list.zip (11 KB)

Data items are the following:
Data itemDescription
ID Internal ID for this ligand
HET_Code HET Code
Link Link to tables in Drug Search (only in simple search)
ChEMBL_ID ChEMBL ID
PrefName Preferred name
HeavyAtoms Number of heavy atoms
FullMWT Full molocular weight
Alogp Value of ALogP
HBA Number of H-bond acceptors
HBD Number of H-bond donors
RotatableBonds Number of ratatable bonds
PSA Polar surface area
ATC_Level1 Classification in ATC level1
ATC_Level2 Classification in ATC level2
ATC_Level3 Classification in ATC level3
ATC_Level4 Classification in ATC level4
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2.7 (Drug Search)Query site list

Data name (Drug Search)Query site list
Description of data contents

The list of binding sites (query) for ligands in (Drug Search) Ligand list
File possum_query_protein.zip (40 KB)

Data items are the following:
Data itemDescription
PocketIndex Internal ID for this binding site
PDB_ID PDB ID for the protein
HET_Code HET code for the ligand
ChainID ID for the chain where the binding site is
Res.No. Residence number for the amino acid where the binding site is
MolName Molecular name of the protein
UniProt UniProt ID for the protein
UniRef50 UniRef50 claster ID for the protein (when it is analysed)
EC EC ID for the protein
CATH CATH ID for the protein
SCOPe SCOPe scope for the ligand
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2.8 (Drug Search)Target site list

Data name (Drug Search)Target site list
Description of data contents

The list of binding sites (target) similar with query sites
File possum_target_protein.zip (844 KB)

Data items are the following:
Data itemDescription
PocketIndex Internal ID for this binding site
PDB_ID PDB ID for the protein
HET_Code HET code for the ligand
ChainID ID for the chain where the binding site is
Res.No. Residence number for the amino acid where the binding site is
MolName Molecular name of the protein
UniProt UniProt ID for the protein
UniRef50 UniRef50 cluster ID for the protein (when it is analysed)
EC EC ID for the protein
CATH CATH ID for the protein
SCOPe SCOPe scope for the ligand
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2.9 (Drug Search)Target ligand list

Data name (Drug Search)Target ligand list
Description of data contents

The list of target sites and binding ligands
File possum_target_ligand.zip (792 KB)

Data items are the following:
Data itemDescription
HET_Code HET Code for the ligand
SimilarPockets Internal id of site binding the ligand
JaccardIndex(MACCS) Jaccard Index between ligand and target site (with MACCS)
JaccardIndex(FP2) Jaccard Index between ligand and target site (with FP2)
InChi_Key InChIKey of binding molocular
CanonicalSmiles Canonical SMILES of binding molocular
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2.10 (Drug Search)Known binding site similarity

Data name (Drug Search)Known binding site similarity
Description of data contents

Similarity data between known binding sites in (Drug Search) query and target sites
File possum_binding_sites_known_similarity.zip (2.4 MB)

Data items are the following:
Data itemDescription
Q:PocketIndex Internal ID for query site
Ｔ:PocketIndex Internal ID for target site
Q:PDB_ID PDB ID for query site
T:PDB_ID PDB ID for target site
Q:HET_Code HED code for query site
T:HET_Code HED code for target site
Q:ChainID ID for the chain where the query site is
T:ChainID ID for the chain where the target site is
Q:Res.No. Residence number for the amino acid where the query site is
T:Res.No. Residence number for the amino acid where the target site is
AlignedLength Length of amino acid alignment
RMSD Root Mean Square Deviation
AminoIdentity Amino acid match rate
Q:MolName Molecular name of the query site
T:MolName Molecular name of the target site
Q:EC EC ID for the query site
T:EC EC ID for the target site
Q:CATH CATH ID for the query site
T:CATH CATH ID for the target site
Q:SCOPe SCOPe ID for the query site
T:SCOPe SCOPe ID for the target site
Q:UniProt UniProt ID for the query site
T:UniProt UniProt ID for the target site
Q:UniRef50 UniRef50 cluster ID for the query site (when it is analysed)
T:UniRef50 UniRef50 cluster ID for the target site (when it is analysed)
EC_Df Different or not between query and target site in EC ID
CATH_Df Different or not between query and target site in CATH ID
SCOPe_Df Different or not between query and target site in SCOPe ID
ChEMBL_Assay Assay data in ChEMBL or none
AlignedResidues Amino acid alignment result
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2.11 (Drug Search)Known binding site similarity

Data name (Drug Search)Known binding site similarity
Description of data contents

Similarity data between known/potential binding sites in (Drug Search) query and target sites
File possum_binding_sites_putative_similarity.zip (5 MB)

Data items are the following:
Data itemDescription
Q:PocketIndex Internal ID for query site
Ｔ:PocketIndex Internal ID for target site
Q:PDB_ID PDB ID for query site
T:PDB_ID PDB ID for target site
Q:HET_Code HED code for query site
T:HET_Code HED code for target site
Q:ChainID ID for the chain where the query site is
T:ChainID ID for the chain where the target site is
Q:Res.No. Residence number for the amino acid where the query site is
T:Res.No. Residence number for the amino acid where the target site is
AlignedLength Length of amino acid alignment
RMSD Root Mean Square Deviation
AminoIdentity Amino acid match rate
Q:MolName Molecular name of the query site
T:MolName Molecular name of the target site
Q:EC EC ID for the query site
T:EC EC ID for the target site
Q:CATH CATH ID for the query site
T:CATH CATH ID for the target site
Q:SCOPe SCOPe ID for the query site
T:SCOPe SCOPe ID for the target site
Q:UniProt UniProt ID for the query site
T:UniProt UniProt ID for the target site
Q:UniRef50 UniRef50 cluster ID for the query site (when it is analysed)
T:UniRef50 UniRef50 cluster ID for the target site (when it is analysed)
EC_Df Different or not between query and target site in EC ID
CATH_Df Different or not between query and target site in CATH ID
SCOPe_Df Different or not between query and target site in SCOPe ID
ChEMBL_Assay Assay data in ChEMBL or none
AlignedResidues Amino acid alignment result
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3. License

Last updated : 2019/03/28

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: "PoSSuM © Tokyo Waterfront, the 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.

2-4-7 Aomi, Koto-ku, Tokyo, 135-0064 Japan
National Institute of Advanced Industrial Science and Technology (AIST)
Kentaro TOMII, PhD

E-mail: k-tomii[at]aist[dot]go[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
2019/03/28 PoSSuM English archive site is opened.
2011/11/01 PoSSuM (http://possum.cbrc.jp/PoSSuM/index.html) is opened.
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5. Literature

Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K.
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.
Nucleic Acids Res. DB issue 2015;43:D392-8.
PMID: 25404129

Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K.
PoSSuM: a database of similar protein-ligand binding and putative pockets.
Nucleic Acids Res. DB issue 2012;40:D541-8.
PMID: 22135290

Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K.
PDB-Scale analysis of known and putative ligand binding sites with structural sketches.
Proteins 2011;80:747-63.
PMID: 22113700

Tabei Y, Uno T, Sugiyama M, Tsuda K.
Single Versus Multiple Sorting for All Pairs Similarity Search.
The 2nd Asian Conference on Machine Learning (ACML2010) 2010.

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6. Contact address

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

2-4-7 Aomi, Koto-ku, Tokyo, 135-0064 Japan
National Institute of Advanced Industrial Science and Technology (AIST)
Kentaro TOMII, PhD

E-mail: k-tomii[at]aist[dot]go[dot]jp

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