:: DESCRIPTION
MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets) is a web server for accurate prediction of true or functional miRNA binding sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sci Rep. 2015 Jan 23;5:8004. doi: 10.1038/srep08004.
MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.
Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z
:: DESCRIPTION
TargetATP is a full-featured GUI application for targeting protein-ATP binding residues in protein sequences, consisting of two parts of local client and remote server.
::DEVELOPER
Pattern Recognition and Bioinformatics Group, Shanghai Jiao Tong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
J Comput Chem. 2013 Apr 30;34(11):974-85. doi: 10.1002/jcc.23219. Epub 2013 Jan 3.
TargetATPsite: a template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.
Yu DJ1, Hu J, Huang Y, Shen HB, Qi Y, Tang ZM, Yang JY.
:: DESCRIPTION
motifbreakR is a package for predicting the disruptiveness Of Single Nucleotide Polymorphisms on transcription factor binding sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.
Coetzee SG, Coetzee GA, Hazelett DJ.
Bioinformatics. 2015 Aug 12. pii: btv470.
:: DESCRIPTION
PS-HomPPI is a sequence-based partner-specific protein-protein interface residue prediction server.
NPS-HomPPI is a sequence-based non-partner-specific protein-protein interface residue prediction server.
::DEVELOPER
Artificial Intelligence Research Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011 Jun 17;12:244. doi: 10.1186/1471-2105-12-244.
HomPPI: a class of sequence homology based protein-protein interface prediction methods.
Xue LC1, Dobbs D, Honavar V.
:: DESCRIPTION
JBD (Joint Binding Deconvolution) uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2006 Aug;24(8):963-70.
High-resolution computational models of genome binding events.
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.
:: DESCRIPTION
eMatchSite is a sequence order-independent algorithm for ligand binding site alignment and matching. It accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures. Furthermore, it tolerates structural distortions in protein models, thus experimentally solved structures are not required.
::DEVELOPER
Computational Systems Biology Group,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.
Brylinski M.
PLoS Comput Biol. 2014 Sep 18;10(9):e1003829. doi: 10.1371/journal.pcbi.1003829.
:: DESCRIPTION
SiTaR (Site Tracking and Recognition) is a novel tool for transcription factor binding site prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SiTaR: a novel tool for transcription factor binding site prediction.
Fazius E, Shelest V, Shelest E.
Bioinformatics. 2011 Oct 15;27(20):2806-11. doi: 10.1093/bioinformatics/btr492.
:: DESCRIPTION
BiSA (Binding sites analyser) is a database driven software and stores all of its data in a relational database management system (RDBMS) such as SQL Server in Windows or PostgreSQL on Linux.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Binding sites analyser (BiSA): software for genomic binding sites archiving and overlap analysis.
Khushi M, Liddle C, Clarke CL, Graham JD.
PLoS One. 2014 Feb 12;9(2):e87301. doi: 10.1371/journal.pone.0087301.
:: DESCRIPTION
ChIPCor is a testing procedure for evaluating the significance of overlapping from a pair of proteins by leveraging information from publicly available data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Measuring the spatial correlations of protein binding sites.
Wei Y, Wu H.
Bioinformatics. 2016 Feb 9. pii: btw058.
:: DESCRIPTION
TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces.
::DEVELOPER
Computational Regulatory Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Lenhard B., Wasserman W.W. (2002)
TFBS: Computational framework for transcription factor binding site analysis.
Bioinformatics 18:1135-1136