ABC 1.3 – Allele-specific Binding from ChIP-Seq

PAComplex is a web server investigating and visualizing both TCR-peptide / peptide-MHC interfaces; furthermore, it provides biological insights of TCR-pMHC binding models.

::DEVELOPER

PAComplex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W254-60. doi: 10.1093/nar/gkr434. Epub 2011 Jun 11.
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.
Liu IH1, Lo YS, Yang JM.

msCentipede 1.0 – Hierarchical Multiscale model for inferring Transcription Factor Binding from Chromatin Accessibility data

msCentipede 1.0

:: DESCRIPTION

msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq)

::DEVELOPER

Anil Raj

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
Python

:: DOWNLOAD

msCentipede

:: MORE INFORMATION

Citation

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M.
PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030.

Uncoupler – Analysis of Coupled Folding and Binding

Uncoupler

:: DESCRIPTION

Uncoupler is a software analysis of coupled folding and binding equilibria by global analysis of temperature dependence isothermal titration calorimetry and CD data.

::DEVELOPER

Mark A. Williams

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Mathematica

:: DOWNLOAD

Uncoupler

:: MORE INFORMATION

Citation

Matthew J. Cliff, Mark A. Williams, David Barford, John E. Ladbury (2005).
Molecular recognition via coupled folding and binding in a TPR domain.
J. Mol. Biol. 346, 717-32.

SAAMBE – Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

SAAMBE

:: DESCRIPTION

SAAMBE (Single Amino Acid Mutation related change of Binding Energy) method addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast (<< 1 minute) modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points.

::DEVELOPER

Professor Emil Alexov Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
Petukh M, Dai L, Alexov E.
Int J Mol Sci. 2016 Apr 12;17(4). pii: E547.

DBChIP 1.36.0 – Differential Binding of Transcription Factor with ChIP-seq

DBChIP 1.36.0

:: DESCRIPTION

DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.

::DEVELOPER

Kun Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
BioCOnductor

:: DOWNLOAD

DBChIP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):121-2. doi: 10.1093/bioinformatics/btr605. Epub 2011 Nov 3.
Detecting differential binding of transcription factors with ChIP-seq.
Liang K1, Keles S.

aPPRove – Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding

aPPRove

:: DESCRIPTION

aPPRove is a computational tool that predicts the interaction of a PPR with its RNA binding site.

::DEVELOPER

SEQ Development Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

aPPRove

:: MORE INFORMATION

Citation

New Phytol. 2011 Jul;191(1):37-47. doi: 10.1111/j.1469-8137.2011.03746.x. Epub 2011 May 9.
The evolution of RNA editing and pentatricopeptide repeat genes.
Fujii S1, Small I.

PANTHER – Novel tool to Predict Small Molecule Binding into Proteins

PANTHER

:: DESCRIPTION

PANTHER is a rapid virtual screening method that can evaluate tens of millions of small molecules into selected protein target in 24 hours

::DEVELOPER

Computational Bioscience Laboratory, University of Jyväskylä

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

PANTHER

:: MORE INFORMATION

Citation

Ultrafast protein structure-based virtual screening with Panther.
Niinivehmas SP, Salokas K, Lätti S, Raunio H, Pentikäinen OT.
J Comput Aided Mol Des. 2015 Sep 25.

JASPAR 2020 – Transcription Factor Binding Profile Database

JASPAR 2020

:: DESCRIPTION

JASPAR is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
R package/BioConductor/BioPython

:: DOWNLOAD

JASPAR for BioConductor

:: MORE INFORMATION

Citation

Fornes O, Castro-Mondragon JA, Khan A, et al.
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res. 2019; doi: 10.1093/nar/gkz1001

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.
Nucleic Acids Res. 2013 Nov 4.

BeAtMuSiC 1.0 – Prediction of Binding Affinity Changes upon Mutations

BeAtMuSiC 1.0

:: DESCRIPTION

The BeAtMuSiC program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. doi: 10.1093/nar/gkt450. Epub 2013 May 30.
BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.
Dehouck Y, Kwasigroch JM, Rooman M, Gilis D.