NAGbinder – Web Server for Predicting N-Acetylglucosamine Binding Sites

NAGbinder

:: 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

NAGbinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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

LPIcom – Analysis, Comparison and Prediction of Protein Ligand Binding Sites

LPIcom

:: DESCRIPTION

LPIcom is a web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank.

::DEVELOPER

LPIcom team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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.

TFBSs 1.0 – Predicting Transcription Factor Binding Sites

TFBSs 1.0

:: 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

  • Web Borowser

:: 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

P2Rank 2.0.1 – Protein-Ligand Binding Site prediction

P2Rank 2.0.1

:: 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

SIRET Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE 8 (Java 1.8) or JRE 11 (Java 11)
  • PyMOL

:: DOWNLOAD

P2Rank

:: 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.

SeqSite 1.0.0 – ChIP-Seq Binding Site Identification

SeqSite 1.0.0

:: 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

SeqSite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C Compiler

:: DOWNLOAD

  SeqSite

:: 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.

MetalionRNA – Metal Ion Binding Site Predictor

MetalionRNA

:: DESCRIPTION

MetalionRNA is a novel bioinformatic method for predicting metal-binding sites in RNA structures.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: 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.

co-evo – Correlated Evolutions of Transcript Factors and their Binding Sites

co-evo

:: DESCRIPTION

co-evo is used to calculate the PCC between the PWM and the protein/domain similarity matrix.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java
  • Perl

:: DOWNLOAD

co-evo

:: MORE INFORMATION

Citation

Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang and Junwen Wang
Correlated evolution of transcription factors and their binding sites.
Bioinformatics. (2011) 27 (21): 2972-2978. doi: 10.1093/bioinformatics/btr503

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

xFITOM

:: 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

TFBSTools 1.10.3 – Transcription Factor Binding Site (TFBS) Analysis

TFBSTools 1.10.3

:: 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.

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.