:: DESCRIPTION
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites and transcription factor profile matrices.
::DEVELOPER
Computational Regulatory Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.
Tan G, Lenhard B.
Bioinformatics. 2016 Jan 21. pii: btw024.
:: DESCRIPTION
SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W441-4. doi: 10.1093/nar/gkq400. Epub 2010 May 19.
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Ren J1, Xie L, Li WW, Bourne PE.
:: DESCRIPTION
PocketMatch is a software for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalidas Yeturu and Nagasuma Chandra(2008)
PocketMatch: A new algorithm to compare binding sites in protein structures
BMC Bioinformatics 2008, 9:543
:: DESCRIPTION
PocketAlign is a web server of comparison of binding sites helps identify functional similarities and also identify drug cross-reactivities
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21.
PocketAlign a novel algorithm for aligning binding sites in protein structures.
Yeturu K, Chandra N.
:: DESCRIPTION
ABS-Scan performs alanaine scanning mutagenesis for a given protein-ligand complex.
::DEVELOPER
Chandra Lab, Dept. of Biochemistry.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.
Anand P, Nagarajan D, Mukherjee S, Chandra N.
Version 2. F1000Res. 2014 Sep 9 [revised 2014 Dec 1];3:214. doi: 10.12688/f1000research.5165.2. eCollection 2014.
:: DESCRIPTION
IDRBind is a protein interface predictor for binding sites of intrinsically disordered protein regions (IDRs), ranging from peptide motifs (i.e., short linear motifs) to molecular recognition features (MoRFs). Differentiating IDRBind from other interface predictors is its emphasis on binding sites of MoRFs, which are long interaction mediating elements within IDRs.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wong ETC, Gsponer J.
Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions.
J Mol Biol. 2019 Aug 9;431(17):3157-3178. doi: 10.1016/j.jmb.2019.06.010. Epub 2019 Jun 15. PMID: 31207240.
:: DESCRIPTION
DBSI (DNA Binding Site Identifier), is a binding site predictor for DNA, and it has also successfully identified binding sites for RNA and heparin.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DBSI Server: DNA Binding Site Identifier.
Sukumar S, Zhu X, Ericksen SS, Mitchell JC.
Bioinformatics. 2016 Jun 3. pii: btw315.
:: DESCRIPTION
FITOM is a computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user.
xFITOM is a fully featured GUI-enabled version of FITOM for Ms-Windows platforms that integrates additional functionality. The program provides an easy to use graphical user interface (GUI) to define all the relevant options for locating binding sites in genetic sequences.
jFITOM is a Java version of FITOM.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Erill, I; O’Neill, M.C.
“A reexamination of information theory-based methods for DNA-binding site identification”
BMC Bioinformatics. 2009 Feb 11;10(1):57
Bhargava, N. & Erill, I. (2010)
“xFITOM: a generic GUI tool to search for transcription factor binding sites”,
Bioinformation 5(2) 49-51
:: DESCRIPTION
BSpred is a neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
S. Mukherjee, Y. Zhang.
Protein-protein complex structure predictions by multimetic threading and template recombination.
Structure. 2011 Jul 13;19(7):955-66.
:: DESCRIPTION
DoGSiteScorer is an automated pocket detection and analysis tool. Size, shape and physico-chemical features of automatically predicted pockets are annotated and incorporated into a support vector machine for druggability estimations.
::DEVELOPER
Center for Bioinformatics (ZBH), University of Hamburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Aug 1;28(15):2074-5. doi: 10.1093/bioinformatics/bts310. Epub 2012 May 23.
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment.
Volkamer A1, Kuhn D, Rippmann F, Rarey M.
