EDCNN -Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network

EDCNN

:: DESCRIPTION

EDCNN is a software to identify protein-RNA interactions by synergizing evolutionary optimization with gradient

::DEVELOPER

EDCNN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

EDCNN

:: MORE INFORMATION

Citation

Wang Y, Yang Y, Ma Z, Wong KC, Li X.
EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
Bioinformatics. 2021 Oct 25:btab739. doi: 10.1093/bioinformatics/btab739. Epub ahead of print. PMID: 34694393.

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.

RBPmap 1.2 – Motifs Analysis and Prediction of RNA Binding Proteins

RBPmap 1.2

:: DESCRIPTION

RBPmap is a computational tool that enables accurate prediction and mapping of RNA binding proteins (RBPs) binding sites on any RNA sequence or list of sequences of interest, provided by the users (as either sequences or genomic coordinates). RBPmap has been developed specifically for mapping RBPs in human, mouse and drosophila melanogaster genomes, though it supports mapping RBP binding sites in other organisms too.

::DEVELOPER

the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RBPmap

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.
RBPmap: a web server for mapping binding sites of RNA-binding proteins.
Paz I, Kosti I, Ares M Jr, Cline M, Mandel-Gutfreund Y

SPOT-Struct-RNA – RNA-binding Protein Prediction from 3D structure

SPOT-Struct-RNA

:: DESCRIPTION

SPOT-Struct-RNA is a sofware for RNA-binding protein prediction from 3D structure

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPOT-Struct-RNA

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Apr;39(8):3017-25. doi: 10.1093/nar/gkq1266. Epub 2010 Dec 22.
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.
Zhao H1, Yang Y, Zhou Y.

SPOT-Seq-RNA – RNA-binding Protein prediction from sequence

SPOT-Seq-RNA

:: DESCRIPTION

SPOT-Seq-RNA is a software for predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPOT-Seq-RNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:119-30. doi: 10.1007/978-1-4939-0366-5_9.
SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.
Yang Y1, Zhao H, Wang J, Zhou Y.

BindUP 1.0 – Predicting DNA and RNA Binding Proteins using Electrostatic Patches

BindUP 1.0

:: DESCRIPTION

BindUP is an automatic server to predict DNA and RNA binding proteins given the three dimensional structure of the protein.

::DEVELOPER

the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.
Paz I, Kligun E, Bengad B, Mandel-Gutfreund Y.
Nucleic Acids Res. 2016 May 19. pii: gkw454.

GraphProt 1.1.4 – Modeling Binding preferences of RNA-binding Proteins

GraphProt 1.1.4

:: DESCRIPTION

GraphProt can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GraphProt

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 22;15(1):R17. [Epub ahead of print]
GraphProt: modeling binding preferences of RNA-binding proteins.
Maticzka D, Lange SJ, Costa F, Backofen R.

CapR 1.1.1 – Revealing Structural Specificities of RNA-binding protein Target Recognition

CapR 1.1.1

:: DESCRIPTION

CapR calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences.

::DEVELOPER

Tsukasa Fukunaga

::REQUIREMENTS

  • Linux
  • Vienna RNA package

:: DOWNLOAD

 CapR

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 21;15(1):R16. doi: 10.1186/gb-2014-15-1-r16.
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.
Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H.

RNApred – Prediction of RNA-binding Proteins

RNApred

:: DESCRIPTION

RNApred is a webserver developed for predicting RNA-binding proteins from their amino acid sequence using different compositional features of proteins.

::DEVELOPER

RNApred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Mol Recognit. 2011 Mar-Apr;24(2):303-13. doi: 10.1002/jmr.1061.
SVM based prediction of RNA-binding proteins using binding residues and evolutionary information.
Kumar M1, Gromiha MM, Raghava GP.