TargetATPsite / TargetATP – Predicting Protein-ATP Binding Site

TargetATPsite /  TargetATP

:: DESCRIPTION

TargetATP is a full-featured GUI application for targeting protein-ATP binding residues in protein sequences, consisting of two parts of local client and remote server.

TargetATPsite is a new sequence-based template-free predictor to identify the Adenosine-5′-triphosphate (ATP) binding sites with machine-learning approaches.

::DEVELOPER

Pattern Recognition and Bioinformatics Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Dong-Jun Yu, Jun Hu, Zhen-Min Tang, Hong-Bin Shen, Jian Yang, and Jing-Yu Yang.
Improving Protein-ATP Binding Residues Prediction by Boosting SVMs with Random Under-Sampling.
Neurocomputing. 2013, 104: 189-199.

J Comput Chem. 2013 Apr 30;34(11):974-85. doi: 10.1002/jcc.23219. Epub 2013 Jan 3.
TargetATPsite: a template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.
Yu DJ1, Hu J, Huang Y, Shen HB, Qi Y, Tang ZM, Yang JY.

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.

TFBIND – Searching Transcription Factor Binding Sites

TFBIND

:: DESCRIPTION

TFBIND is a software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)).

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 1999 Jul-Aug;15(7-8):622-30.
Estimating transcription factor bindability on DNA.
Tsunoda T, Takagi T.

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