DNAbinder – Prediction of DNA-binding Proteins

DNAbinder

:: DESCRIPTION

DNAbinder is a webserver developed for predicting DNA-binding proteins from their amino acid sequence using various compositional features of proteins.

::DEVELOPER

DNAbinder Team .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 27;8:463.
Identification of DNA-binding proteins using support vector machines and evolutionary profiles.
Kumar M, Gromiha MM, Raghava GP.

G=MAT – Linking Transcription Factor Expression with DNA Binding

G=MAT

:: DESCRIPTION

G=MAT is a computational method for finding putative associations between transcription factors and motifs.

::DEVELOPER

Bioinformatics, Algorithmics and Data Mining Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMAT-Web

:: MORE INFORMATION

Citation

PLoS One. 2011 Jan 31;6(1):e14559. doi: 10.1371/journal.pone.0014559.
G = MAT: linking transcription factor expression and DNA binding data.
Tretyakov K1, Laur S, Vilo J.

FFS – Database of Drosophila TF DNA Binding Specificities

FFS

:: DESCRIPTION

FFS (FlyFactorSurvey, Fly Factor Survey) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Jan;39(Database issue):D111-7. doi: 10.1093/nar/gkq858.
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.
Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH.

DBS-PRED – Prediction of DNA-binding in proteins using Neural Networks

DBS-PRED

:: DESCRIPTION

DBS-PRED predicts the DNA-binding in a protein from their sequence information. Two neighbours of each residue are taken as the input information and using information from known binding sites of proteins, probable binding sites are predicted. Amino acid composition is taken as the input information for the prediction of DNA-binding probability of a protein.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Analysis and Prediction of DNA-binding proteins and their binding residues based on composition, sequence and structure information.
by Shandar Ahmad, M. Michael Gromiha and Akinori Sarai
Bioinformatics 20 (2004) 477-486

DNAbind – DNA Binding Protein prediction

DNAbind

:: DESCRIPTION

DNAbind server predicts whether a protein is DNA-binding from its structure and/or sequence.

::DEVELOPER

the Institute of Enzymology, Hungarian Academy of Sciences.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Szilagyi A, Skolnick J:
Efficient prediction of nucleic acid binding function from low-resolution protein structures.
J Mol Biol. 2006 May 5;358(3):922-33. Epub 2006 Mar 10