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Pocketome specifications


Unique identifier OMICS_03833
Name Pocketome
Restrictions to use None
Maintained No

Publication for Pocketome

Pocketome citations


A genome wide structure based survey of nucleotide binding proteins in M. tuberculosis

Sci Rep
PMCID: 5624866
PMID: 28970579
DOI: 10.1038/s41598-017-12471-8

[…] ite signatures or structural motifs were derived for each site-type. The derived motifs were also determined to be specific towards NTP recognition. Each motif was used individually to query the M.tb pocketome, which is a dataset of 13,858 pockets, derived as previously described. To obtain all the putative small-molecule binding pockets in M.tb, a structural modeling of the M.tb proteome was requ […]


Normal Modes Expose Active Sites in Enzymes

PLoS Comput Biol
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] tic data were developed [–]. Several webservers of ligand binding sites have also been constructed and may be used to infer unknown ligand binding sites based on homology and other attributes such as Pocketome [], FunFold [], scPDB [], IBIS [], Multibind [], fPop [], and FINDSITE []. To date however, no comprehensive study comparing geometry based techniques has been performed.Normal-mode analysis […]


Mapping the 3D structures of small molecule binding sites

J Cheminform
PMCID: 5395517
DOI: 10.1186/s13321-016-0180-0

[…] arity between protein–ligand binding sites include Relibase, a database of known protein–ligand binding sites []; the sc-PDB, an annotated database of druggable binding sites from the PDB []; and the Pocketome, an encyclopedia of conformational ensembles of druggable binding sites []. While each of these tools provides an assessment of similarity between binding sites, the potential for identifyin […]


Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

PMCID: 4901368
PMID: 27074285
DOI: 10.1021/acs.chemrev.5b00631

[…] s draw on large structural and genomic databases to determine binding-pocket locations based on sequence and overall structure rather than pocket shape. Algorithms such as 3DLigandSite, FINDSITE, and Pocketome infer these locations by querying existing databases for ligand-bound proteins that are structurally similar to the target protein. These algorithms work particularly well when the target pr […]


Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

Sci Rep
PMCID: 5376175
PMID: 25220818
DOI: 10.1038/srep06356

[…] subset of protein-ligand complexes in PDB, from which expected clustering pattern was obtained as shown in (see methodology section on validation). We refer to the 29 clusters obtained from the Mtb pocketome as ‘sets’ of proteins containing similar binding sites within each. By considering one representative of each set and adding onto the singletons, we find that the pocketome contains 6584 dif […]


Drug Like Protein–Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Mol Inform
PMCID: 4160817
PMID: 25254076
DOI: 10.1002/minf.201400040

[…] pockets have been developed[] and some examples of recently reported approaches include PocketAnnotate,[] APoc[] and SiteComp.[] All these pockets have been stored in databases like for instance the pocketome.[] Somewhat related, in a recent study, interfaces were defined and clustered leading to the identification of 22 604 unique interface structures in the PDB.[] […]


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Pocketome institution(s)
UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA

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