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PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K - Nucleic Acids Res. (2014)

Bottom Line: This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery.Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM.Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.

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Table of binding pockets detected to be similar to the query pockets (A). Similar pocket pairs are displayed in two tables, depending on whether the similar pocket is a known binding pocket (B) or a putative pocket (C).
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Figure 4: Table of binding pockets detected to be similar to the query pockets (A). Similar pocket pairs are displayed in two tables, depending on whether the similar pocket is a known binding pocket (B) or a putative pocket (C).

Mentions: In the fourth and last section, one can retrieve all of the binding pockets on both the query and target sides (Figure 4A), as well as all of the similarity details between them (Figure 4B and C). For several query ligands, such as kinase inhibitors, the number of similar pocket pairs exceeds 10 000, which is difficult to display in a web page. Therefore, we generated a subset of pocket pairs in the following manner. Presuming that a query pocket is associated with UniProt ID P1 and HET code H1, and that one similar pocket was identified as associated with UniProt ID P2 and HET code H2, if multiple similar pocket pairs were identified between (P1, H1) and (P2, H2), then only the pair with the longest aligned length is selected. For putative pockets, the HET code H2 was ignored. If the interaction between a query ligand and an identified target receptor has been tested by any binding assay, then we assigned a flag ‘Yes’ to the similarity pair in the last column (Figure 4B and C). ChEMBL assay information was retrieved via the TargetMine data warehouse (22). Users can download not only the subset displayed in the tables, but also all pairs at the end of the tables (Figure 4B and C).


PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K - Nucleic Acids Res. (2014)

Table of binding pockets detected to be similar to the query pockets (A). Similar pocket pairs are displayed in two tables, depending on whether the similar pocket is a known binding pocket (B) or a putative pocket (C).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383952&req=5

Figure 4: Table of binding pockets detected to be similar to the query pockets (A). Similar pocket pairs are displayed in two tables, depending on whether the similar pocket is a known binding pocket (B) or a putative pocket (C).
Mentions: In the fourth and last section, one can retrieve all of the binding pockets on both the query and target sides (Figure 4A), as well as all of the similarity details between them (Figure 4B and C). For several query ligands, such as kinase inhibitors, the number of similar pocket pairs exceeds 10 000, which is difficult to display in a web page. Therefore, we generated a subset of pocket pairs in the following manner. Presuming that a query pocket is associated with UniProt ID P1 and HET code H1, and that one similar pocket was identified as associated with UniProt ID P2 and HET code H2, if multiple similar pocket pairs were identified between (P1, H1) and (P2, H2), then only the pair with the longest aligned length is selected. For putative pockets, the HET code H2 was ignored. If the interaction between a query ligand and an identified target receptor has been tested by any binding assay, then we assigned a flag ‘Yes’ to the similarity pair in the last column (Figure 4B and C). ChEMBL assay information was retrieved via the TargetMine data warehouse (22). Users can download not only the subset displayed in the tables, but also all pairs at the end of the tables (Figure 4B and C).

Bottom Line: This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery.Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM.Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.

Show MeSH
Related in: MedlinePlus