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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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Schematic view of the PoSSuMds approach for screening ligand analogs and their receptor proteins. Ligands, binding pockets and receptors are shown in red, green and cyan, respectively.
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Figure 1: Schematic view of the PoSSuMds approach for screening ligand analogs and their receptor proteins. Ligands, binding pockets and receptors are shown in red, green and cyan, respectively.

Mentions: For any given drug compound, a challenging task in structural bioinformatics is to find related (and biologically relevant) compounds and target proteins. Our approach is to collect a set of binding sites similar to the pockets to which the query ligand is known to bind. This type of approach is useful for retrieving various ligand analogs, such as natural ligands, inhibitors and metabolites, and also for obtaining potential target proteins (Figure 1).


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)

Schematic view of the PoSSuMds approach for screening ligand analogs and their receptor proteins. Ligands, binding pockets and receptors are shown in red, green and cyan, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Schematic view of the PoSSuMds approach for screening ligand analogs and their receptor proteins. Ligands, binding pockets and receptors are shown in red, green and cyan, respectively.
Mentions: For any given drug compound, a challenging task in structural bioinformatics is to find related (and biologically relevant) compounds and target proteins. Our approach is to collect a set of binding sites similar to the pockets to which the query ligand is known to bind. This type of approach is useful for retrieving various ligand analogs, such as natural ligands, inhibitors and metabolites, and also for obtaining potential target proteins (Figure 1).

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