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Protocols

pevoSOAR specifications

Information


Unique identifier OMICS_13747
Name pevoSOAR
Alternative name Pocketbased EVOlutionary Search Of Amino acid Residues
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Jie Liang

Publication for Pocketbased EVOlutionary Search Of Amino acid Residues

pevoSOAR citations

 (5)
library_books

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

2013
PLoS One
PMCID: 3651201
PMID: 23675414
DOI: 10.1371/journal.pone.0062535

[…] ov Model (HMM) methods , , Evolutionary Trace , INTREPID , Phylofacts , , and Bayesian Monte Carlo inference . that combine sequence and structural information include EFICAz , , SOIPPA –, DISCERN , PevoSOAR , and AnnoLite and can provide improvements to sequence based methods alone. The success of global similarity-based techniques depends largely on the ability to distinguish conservation patt […]

library_books

Accurate Protein Structure Annotation through Competitive Diffusion of Enzymatic Functions over a Network of Local Evolutionary Similarities

2010
PLoS One
PMCID: 3001439
PMID: 21179190
DOI: 10.1371/journal.pone.0014286

[…] relevant , , other methods focus on just a few but presumably key residues. For example, residues could be taken from concave protein regions since these are more likely to be functionally important (pevoSoar) . More generally, residues can be taken from putative functional sites in their relative three-dimensional (3D) configuration to create 3D templates: composite structural motifs of a few ami […]

library_books

The LabelHash algorithm for substructure matching

2010
BMC Bioinformatics
PMCID: 2996407
PMID: 21070651
DOI: 10.1186/1471-2105-11-555

[…] h 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 statistics used to determine significance of match. Representatio […]

library_books

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

2010
BMC Bioinformatics
PMCID: 2885373
PMID: 20459833
DOI: 10.1186/1471-2105-11-242

[…] n 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 substructure is critical and the (successful) performance of motif-driven subst […]

call_split

Drug Discovery Using Chemical Systems Biology: Identification of the Protein Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

2009
PLoS Comput Biol
PMCID: 2676506
PMID: 19436720
DOI: 10.1371/journal.pcbi.1000387
call_split See protocol

[…] ,.Besides SMAP used in this study, a number of web servers for ligand binding site search are available, for example, SiteEngine , SitesBase ,, CavBase –, SuMo , PdbSiteScan , eF-Site ,, pvSOAR , and pevoSOAR . Compared with these servers, SMAP has several distinguishing features making it particularly suitable for identifying off-targets on a structural genome-wide scale. First, SMAP does not req […]

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pevoSOAR institution(s)
Department of Bioengineering, University of Illinois at Chicago, SEO, Chicago, IL, USA
pevoSOAR funding source(s)
This work is supported by grants from NSF (DBI-0646035 and DMS-0800257), NIH (GM079804-01A1 and GM081682), and ONR (N000140310329).

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