SiteEngine protocols

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SiteEngine specifications

Information


Unique identifier OMICS_10537
Name SiteEngine
Interface Web user interface
Restrictions to use None
Input data Two protein structures.
Output data A superimposition and a list of physicochemical properties.
Output format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Alexandra Shulman-Peleg <>

Publications for SiteEngine

SiteEngine in pipeline

2012
PMCID: 3408369
PMID: 22536854
DOI: 10.1186/1472-6807-12-5

[…] in the mammoth program package []. all of the pairwise alignments were performed with the default parameters. the active sites were compared using a geometric hashing algorithm implemented in siteengine []., the f-measure is defined as a harmonic mean of both precision and recall that measures the extent to which a cluster contains only enzymes of particular ec classes and all enzymes […]


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SiteEngine in publications

 (9)
PMCID: 4565107
PMID: 26356630
DOI: 10.1186/1752-0509-9-S5-S3

[…] methods, namely ppi-pred, pinup, ppisp, promate, and sppider., in addition, several structural algorithms have also been used to identify binding sites, through analyzing surface structures. siteengine [] recognizes surface regions of a testing protein that are similar to some known binding sites, using geometric hashing triangles. probis [] predicts interface residues by local surface […]

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

[…] with constraints. jess matched structure templates based on constrained logic programming. cavbase and ef-site used clique-based method , to match structure templates formed by surface patches. siteengine , , sitesbase , , multibind and tess applied geometric hashing algorithms , , , , , to match protein surfaces and binding sites. in a study by weskamp et al. , clique detection […]

PMCID: 3408369
PMID: 22536854
DOI: 10.1186/1472-6807-12-5

[…] of matched pairs (wild/wild or mutant/mutant) and mismatched pairs (wild/mutant) for each enzyme compared to the distance measure (the complement 100 minus the match score) obtained using siteengine (table ). as shown in table , most of the pairs were agglomerated within a euclidean distance of 222, and the rdfs were successful in revealing their similarity. the pairs from mdh_ecoli […]

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

[…] and determine functional similarity. a wide variety 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 […]

PMCID: 2922380
PMID: 20808948
DOI: 10.1371/journal.pone.0012214

[…] a significant similarity score between 1yhs and 1aux active sites (pocketmatch pmscore  = 50.79; fuzcav score  = 0.160). conversely, two state-of-the-art full atom-matching methods (sitesbase , siteengine ) failed in finding the same binding sites similar (siteengine match score  = 18.71; no output for sitesbase). siteengine notably fails to fit the pair of glutamic acid residues (glu121 […]


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SiteEngine institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology NCI-Frederick, Frederick, MD, USA
SiteEngine funding source(s)
Supported by Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

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