:: DESCRIPTION
TFBIND is a software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)).
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 1999 Jul-Aug;15(7-8):622-30.
Estimating transcription factor bindability on DNA.
Tsunoda T, Takagi T.
:: DESCRIPTION
NAGbinder is a web server developed for predicting NAG interacting residues in a protein from its primary sequence. This server has following two modules; Sequence based module;PSSM based Module;
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.
Patiyal S, Agrawal P, Kumar V, Dhall A, Kumar R, Mishra G, Raghava GPS.
Protein Sci. 2019 Oct 25. doi: 10.1002/pro.3761
:: DESCRIPTION
LPIcom is a web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
A web server for analysis, comparison and prediction of protein ligand binding sites.
Singh H, Srivastava HK, Raghava GP.
Biol Direct. 2016 Mar 25;11(1):14. doi: 10.1186/s13062-016-0118-5.
:: DESCRIPTION
TFBSs is a web server for Predicting transcription factor binding sites.
::DEVELOPER
The Li’s Group of Theoretical Biophysics and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Guo-liang Fan and Qianzhong Li, Keli Yang,
TFBSs: a web server for Predicting transcription factor binding sites.
2012 IEEE International Conference on Cyber Technology in Automation, Control, and Intelligent Systems (CYBER), 2012,1:65-68
:: DESCRIPTION
P2Rank is a machine learning based method for prediction of ligand binding sites from protein structure. P2Rank uses Random Forests classifier to infer ligandability of local chemical neighborhoods near the protein surface which are represented by specific near-surface points and described by aggregating physico-chemical features projected on those points from neighboring protein atoms. The points with high predicted ligandability are clustered and ranked to obtain the resulting list of binding site predictions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.
Krivák R, Hoksza D.
J Cheminform. 2018 Aug 14;10(1):39. doi: 10.1186/s13321-018-0285-8.
:: DESCRIPTION
SeqSite was developed for detecting transcription factor binding sites from ChIP-seq data.SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Xi Wang and Xuegong Zhang.
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.
BMC Systems Biology, 5(Suppl 2):S3.
:: DESCRIPTION
MetalionRNA is a novel bioinformatic method for predicting metal-binding sites in RNA structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Computational methods for prediction of RNA interactions with metal ions and small organic ligands.
Philips A, Łach G, Bujnicki JM.
Methods Enzymol. 2015;553:261-85. doi: 10.1016/bs.mie.2014.10.057.
:: DESCRIPTION
inSite (interactive site viewer) is a tool for interactively visualizing binding sites along multiple genomic regions. Different types of transcription factors are encoded with color with a user-defined, interactive color legend.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BSG is a collection of programs used to construct and analyze Binding Site Graphs. Overall,the analysis is a two step process that can be performed on separate computers. First, ensemble Gibbs sampling is performed, preferably on a massively parallel computer, and the results are collected. The resulting output files are then compressed (using gzip) to conserve disk space. Then, in a second step, the compressed output files are analyzed and predictions are made
::DEVELOPER
Bioinformatics and Evolution of Systems Laboratory
:: SCREENSHOTS
n/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Timothy E Reddy, Charles DeLisi, Boris E Shakhnovich
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
PLoS Comput Biol 3(5): e90. doi:10.1371/journal.pcbi.0030090
:: DESCRIPTION
The Protemot (Protein motif) web server predicts protein binding sites based on the interaction templates automatically extracted from the compound crystals in the Protein Data Bank (PDB).
::DEVELOPER
Molecular Biomedical Informatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W303-9.
Protemot: prediction of protein binding sites with automatically extracted geometrical templates.
Chang DT, Weng YZ, Lin JH, Hwang MJ, Oyang YJ.