IDRBind – Protein Interface Predictor for Binding Sites of intrinsically disordered protein regions

IDRBind

:: 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

Gsponer Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: 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.

DBSI – DNA Binding Site Predictor

DBSI

:: 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

Mitchell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DBSI

:: MORE INFORMATION

Citation

DBSI Server: DNA Binding Site Identifier.
Sukumar S, Zhu X, Ericksen SS, Mitchell JC.
Bioinformatics. 2016 Jun 3. pii: btw315.

TFBSTools 1.30.0 – Transcription Factor Binding Site (TFBS) Analysis

TFBSTools 1.30.0

:: DESCRIPTION

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites and transcription factor profile matrices.

::DEVELOPER

Ge Tan <ge.tan09 at imperial.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R/BioConductor

:: DOWNLOAD

 TFBSTools

:: MORE INFORMATION

Citation

TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.
Tan G, Lenhard B.
Bioinformatics. 2016 Jan 21. pii: btw024.

FiToM / xFITOM / jFITOM 201605 – Detection of Binding Sites in DNA or RNA Sequences

FiToM / xFITOM / jFITOM 201605

:: 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

the Erill Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

FITOM , xFITOM , jFITOM

:: 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

BSpred – Predict Binding Site of Proteins

BSpred

:: 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

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  BSpred

:: 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.

DoGSiteScorer 2.0 – Binding Site Prediction, analysis and Druggability Assessment

DoGSiteScorer 2.0

:: 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

  • Windows / Linux

:: DOWNLOAD

DoGSiteScorer

:: 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.

LIBRA v1 / LIBRA+ / LIBRAWA – Ligand Binding site Recognition Application

LIBRA v1 / LIBRA+ / LIBRAWA

:: DESCRIPTION

LIBRA is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites.

LIBRA+ is an upgraded version of LIBRA, a tool that, given a protein’s structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by LIBRA+ is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. For this purpose, the algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively derived from the Catalytic Site Atlas and the Protein Data Bank.

LIBRA Web Application is an online portal where users can exploit LIBRA+’s capabilities in recognizing the presence and identity of active sites and/or ligand binding sites given a protein’s structural model. With a free registration, users are given a personal space where they can launch and schedule multiple recognitions, check out the resulting three-dimensional alignments and browse ligand clusters. Results produced in LIBRAWA are backward-compatible with LIBRA+ and can thus be exported in LIBRA+’s format to be accessed offline from the desktop application.

::DEVELOPER

the Theoretical Biology and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 LIBRA / LIBRA+

:: MORE INFORMATION

Citation

Toti D, Viet Hung L, Tortosa V, Brandi V, Polticelli F.
LIBRA-WA: a web application for ligand binding site detection and protein function recognition.
Bioinformatics. 2018 Mar 1;34(5):878-880. doi: 10.1093/bioinformatics/btx715. PMID: 29126218; PMCID: PMC6192203.

LIBRA: LIgand Binding site Recognition Application.
Viet Hung L, Caprari S, Bizai M, Toti D, Polticelli F.
Bioinformatics. 2015 Aug 26. pii: btv489.

MICSA – Identification of Transcription Factor binding sites in ChIP-Seq data

MICSA

:: DESCRIPTION

MICSA (Motif Identification for ChIP-Seq Analysis) is package for the identification of transcription factor binding sites in ChIP-Seq data

::DEVELOPER

Boeva lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 MICSA

:: MORE INFORMATION

Citation:

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.
Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.
Nucleic Acids Res. 2010 Jun;38(11):e126. Epub 2010 Apr 7.

motifStack 1.34.0 – Visualization of Motif Alignment and the analysis of Transcription Factor Binding site Evolution

motifStack 1.34.0

:: DESCRIPTION

motifStack is a package for the visualization of the alignment of motifs as a phylogenetic tree in different layout types. This tool facilitates the analysis of binding site diversity and conservation within families of TFs and the evolution of TFs among different species. motifStack can align DNA motifs; generate motif signatures for closely related motifs; and plot aligned motifs as a stack, a linear or a radial tree, or a word cloud of sequence logos. Different parameter settings can be used to generate diverse types of plots with color schema highlighting important data features.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

motifStack

:: MORE INFORMATION

Citation:

Ou J, Wolfe SA, Brodsky MH, Zhu LJ.
visualization of motif alignment and the analysis of transcription factor binding site evolution for the analysis of transcription factor binding site evolution.
Nat Methods. 2018 Jan 3;15(1):8-9. doi: 10.1038/nmeth.4555. PMID: 29298290.

ConSite – Transcription Factor Binding Site Detection using Phylogenetic Footprinting

ConSite

:: DESCRIPTION

ConSite explores transcription factor binding sites shared by two genomic sequences

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.
ConSite: web-based prediction of regulatory elements using cross-species comparison.
Sandelin A, Wasserman WW, Lenhard B.