Tag: DNA-binding Protein

DeepDRBP-2L – Genome Annotation predictor for identifying DNA-binding proteins and RNA-binding proteins

DeepDRBP-2L

:: DESCRIPTION

DeepDRBP-2L is a new computational predictor for identifying DBPs, RBPs and DRBPs by combining Convolutional Neural Network (CNN) and the Long Short-Term Memory (LSTM).

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Zhang J, Chen Q, Liu B.
DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1451-1463. doi: 10.1109/TCBB.2019.2952338. Epub 2021 Aug 6. PMID: 31722485.

iDRBP_MMC – Identifying DNA-binding proteins and RNA-binding proteins

iDRBP_MMC

:: DESCRIPTION

iDRBP_MMC is a new sequence-based computational predictor for identifying DNA-binding proteins and RNA-binding proteins based on multi-label learning model and motif-based convolutional neural network.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

iDRBP_MMC

:: MORE INFORMATION

Citation

Zhang J, Chen Q, Liu B.
iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.
J Mol Biol. 2020 Nov 6;432(22):5860-5875. doi: 10.1016/j.jmb.2020.09.008. Epub 2020 Sep 11. PMID: 32920048.

enDNA-Prot – Identification of DNA-binding Proteins by Applying Ensemble Learning

enDNA-Prot

:: DESCRIPTION

enDNA-Prot is a web server for DNA-binding protein identification by employing the ensemble learning technique.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ruifeng Xu, Jiyun Zhou, Bin Liu, et al.,
“enDNA-Prot: Identification of DNA-binding Proteins by Applying Ensemble Learning,”
BioMed Research International, Vol. 2014, Article ID 294279, 10 pages, 2014, doi:10.1155/2014/294279

iDNAPro-PseAAC – DNA Binding Protein Identification

iDNAPro-PseAAC

:: DESCRIPTION

iDNAPro-PseAAC is a web server of DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation.
Liu B, Wang S, Wang X.
Sci Rep. 2015 Oct 20;5:15479. doi: 10.1038/srep15479.

PSSM-DT – Identifying DNA-binding proteins by combining Support Vector Machine and PSSM Distance Transformation

PSSM-DT

:: DESCRIPTION

SVM-PSSM-DT is a web server for for identifying the DNA-binding proteins by combining Support Vector Machine and PSSM Distance Transformation.

::DEVELOPER

Bin Liu’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2015;9 Suppl 1:S10. doi: 10.1186/1752-0509-9-S1-S10. Epub 2015 Feb 6.
Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.
Xu R, Zhou J, Wang H, He Y, Wang X, Liu B.

iDNA-Prot|dis – Identifying DNA-binding Proteins

iDNA-Prot|dis

:: DESCRIPTION

iDNA-Prot|dis is a novel predictor which was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) vector.

::DEVELOPER

Liu Lab , Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition.
Liu B, Xu J, Lan X, Xu R, Zhou J, Wang X, Chou KC.
PLoS One. 2014 Sep 3;9(9):e106691. doi: 10.1371/journal.pone.0106691. eCollection 2014.

iDBPs – Identification of DNA Binding Proteins (DBPs) for Proteins with known 3D-structure

iDBPs

:: DESCRIPTION

The iDBPs server was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure

::DEVELOPER

The Ben-Tal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Mar 1;26(5):692-3. doi: 10.1093/bioinformatics/btq019. Epub 2010 Jan 19.
iDBPs: a web server for the identification of DNA binding proteins.
Nimrod G, Schushan M, Szilágyi A, Leslie C, Ben-Tal N.

iDNA-Prot – Predicting DNA-binding proteins

iDNA-Prot

:: DESCRIPTION

The web-server iDNA-Prot was establish for identifying uncharacterized proteins as DNA-binding protiens or non DNA-binding proteins according to their sequences information alone.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(9):e24756. doi: 10.1371/journal.pone.0024756. Epub 2011 Sep 15.
iDNA-Prot: identification of DNA binding proteins using random forest with grey model.
Lin WZ1, Fang JA, Xiao X, Chou KC.

newDNA-Prot – DNA Binding Protein Predict Software

newDNA-Prot

:: DESCRIPTION

newDNA-Prot will predict the DNA-binding proteins when input a protein sequence (Fasta format).

::DEVELOPER

newDNA-Prot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • fortran-windows

:: DOWNLOAD

newDNA-Prot

:: MORE INFORMATION

Citation

newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J.
Comput Biol Chem. 2014 Oct;52:51-9. doi: 10.1016/j.compbiolchem.2014.09.002.