Tag: Binding Site

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.

iPPBS-PseAAC – Prediction of Protein-Protein Binding Sites

iPPBS-PseAAC

:: DESCRIPTION

The web-server iPPBS-PseAAC is used to predict the Protein-Protein Binding Sites(PPBS).

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition.
Jia J, Liu Z, Xiao X, Liu B, Chou KC.
J Biomol Struct Dyn. 2015 Sep 16:1-38

FOOTER 2.0 – Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting

FOOTER 2.0

:: DESCRIPTION

FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

PocketAnalyzerPCA 1.30 – Pocket-space Maps to Identify novel Binding-site Conformations in Proteins

PocketAnalyzerPCA 1.30

:: DESCRIPTION

PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PocketAnalyzerPCA

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Oct 24;51(10):2666-79. doi: 10.1021/ci200168b. Epub 2011 Sep 30.
Pocket-space maps to identify novel binding-site conformations in proteins.
Craig IR1, Pfleger C, Gohlke H, Essex JW, Spiegel K.

TFBS Evo 1.0 – Tracing the Evolution of Lineage-specific Transcription Factor Binding Sites

TFBS Evo 1.0

:: DESCRIPTION

TFBS Evo is a model which traces the evolution of lineage-specific transcription factor binding sites without relying on detailed base-by-base cross-species alignments.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TFBS Evo

:: MORE INFORMATION

Citation

Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
Yokoyama KD, Zhang Y, Ma J.
PLoS Comput Biol. 2014 Aug 21;10(8):e1003771. doi: 10.1371/journal.pcbi.1003771.

3DLigandSite – Ligand Binding Site Prediction Server

3DLigandSite

:: DESCRIPTION

3DLigandSite is a server that automates a successful manual method for the prediction of protein ligand binding residues in CASP8.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W469-73. doi: 10.1093/nar/gkq406. Epub 2010 May 31.
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA, Sternberg MJ.

Superficial 1.2 – Identification of Potential Epitopes or Binding Sites

Superficial 1.2

:: DESCRIPTION

SUPERFICIAL (Surface scan) is a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions. Superficial (Surface scan) scan the surface of proteins, find binding sites etc.

::DEVELOPER

Structural Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Superficial

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Sep 9;6:223.
SUPERFICIAL–surface mapping of proteins via structure-based peptide library design.
Goede A, Jaeger IS, Preissner R.