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SitesBase specifications


Unique identifier OMICS_21181
Name SitesBase
Restrictions to use None
Database management system MySQL
Community driven No
User data submission Not allowed
Version 2.0
Maintained No


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Publication for SitesBase

SitesBase 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

[…] alignment served as a better tool to capture similarities for proteins like Rv0079, Rv1173, Rv2761c, and many others. Existing tools for identifying similarities at the binding sites like ProBis and SitesBase failed to capture the similarities for some of the top-ranking hits in our study, and also, for some proteins like Rv1379, and Rv1843c which are reported in literature to be NTP binding. Thu […]


Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

PLoS One
PMCID: 3651201
PMID: 23675414
DOI: 10.1371/journal.pone.0062535

[…] h algorithm , , along with impressive optimizations at the hardware and software level to improve performance, and is among the fastest procedures reported. Other geometric hashing approaches include SitesBase , and GIRAF . The success of template matching methods led to the important recognition that a high quality database of enzymatic sites is needed. This recognition motivated the development […]


Protein Surface Matching by Combining Local and Global Geometric Information

PLoS One
PMCID: 3398928
PMID: 22815760
DOI: 10.1371/journal.pone.0040540

[…] ch radius is that the upper bound on the RMSD calculated from the matched atoms of two binding sites will be equal to the search radius.The geometric hashing algorithm employed in the construction of SitesBase and other methods (see Introduction for references) has some similarity to our algorithm. However, there are a number of key distinctions. First, we use the Hungarian algorithm to find the s […]


The LabelHash algorithm for substructure matching

BMC Bioinformatics
PMCID: 2996407
PMID: 21070651
DOI: 10.1186/1471-2105-11-555

[…] iety of substructure matching methods have been proposed, such as: TESS [], SPASM [], CavBase [], eF-site [], ASSAM [], PINTS [], Jess [], SuMo [], SiteEngine [], Query3 D [], ProFunc [], ProKnow [], SitesBase [], GIRAF [], MASH [], SOIPPA [,], FEATURE [], and pevoSOAR []. These methods mainly differ in (1) the representation of structural motifs, (2) the motif matching algorithm, and (3) the stat […]


Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair Wise Binding Site Similarity Measurements

PLoS One
PMCID: 2922380
PMID: 20808948
DOI: 10.1371/journal.pone.0012214
call_split See protocol

[…] 1yhs (human Pim-1 kinase) were retrieved from the sc-PDB website ( and compared with the in-house FuzCav algorithm with default parameters . Web interfaces to SitesBase (, SiteEngine ( and PocketMatch ( were used to compare the […]


Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

BMC Bioinformatics
PMCID: 2885373
PMID: 20459833
DOI: 10.1186/1471-2105-11-242

[…] ics with the motif []. Diverse approaches to motif search and/or comparison have been developed and include: SPASM [], ASSAM [], PINTS [], Jess [], SiteEngine [], Query3D [], ProFunc [,], ProKnow [], SitesBase [], GIRAF [], MASH [], LabelHash [], SOIPPA [], FEATURE [], and pevoSOAR [] to name a few. In general, designing high-quality motifs that accurately capture the functional essence of a subst […]


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SitesBase institution(s)
Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
SitesBase funding source(s)
Supported by the BBSRC (grant B18760).

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