Interactions between proteins and RNA play essential roles for life. For example, protein-RNA interactions mediate RNA metabolic processes such as splicing, polyadenylation, messenger RNA stability, localization and translation (Tuschl, 2003). Furthermore, many of these…

Protein-RNA interaction analysis (omic data)

ProNIT ProNIT

ProNIT

Provides experimentally determined thermodynamic interaction data between…

Provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.

Desktop app
Joint Evolutionary… Joint Evolutionary Trees

JET Joint Evolutionary Trees

Detects very different types of interactions of a protein with another protein,…

Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary…

Web app
RNAProSite RNAProSite

RNAProSite

We designed two structural features (residue electrostatic surface potential…

We designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the…

Web app
BindUP BindUP

BindUP

Predicts DNA and RNA binding proteins using a non-homology-based approach.…

Predicts DNA and RNA binding proteins using a non-homology-based approach. BindUP is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP…

Desktop app
PRNAclass PRNAclass

PRNAclass

A protein local structure multiple alignment algorithm to identify the main…

A protein local structure multiple alignment algorithm to identify the main groups of protein-RNA binding pockets. PRNAclass identifies the structure motifs of protein-RNA binding sites in the form…

Desktop app
A A A RNAcommender RNAcommender

RNAcommender

A tool for genome-wide recommendation of RNA-protein interactions. RNAcommender…

A tool for genome-wide recommendation of RNA-protein interactions. RNAcommender is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the…

Desktop app
APRICOT APRICOT

APRICOT

A computational pipeline for the sequence-based identification and…

A computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein…

Desktop app
RBRIdent RBRIdent

RBRIdent

A classifier to identify the RNA-binding residues. In an independent benchmark…

A classifier to identify the RNA-binding residues. In an independent benchmark test, RBRIdent achieved an accuracy of 76.79%, Matthews correlation coefficient of 0.3819 and F-measure of 75.58%,…

Web app
Prediction of… Prediction of RNA-Binding Proteins

PRBP Prediction of RNA-Binding Proteins

Predicts RNA-binding proteins using the information of predicted RNA-binding…

Predicts RNA-binding proteins using the information of predicted RNA-binding residues in conjunction with a random forest based method. For a given protein, we first predict its RNA-binding residues…

Desktop app
integrative… integrative Orthogonality-regularized Nonnegative…

iONMF integrative Orthogonality-regularized Nonnegative Matrix Factorization

Integrates multiple data sources and discover non-overlapping, class-specific…

Integrates multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and…

Web app
Hot Spot at… Hot Spot at Protein-RNA interacing surface

HotSPRing Hot Spot at Protein-RNA interacing surface

A web server to predict the host spots in RNA binding proteins (RBPs). The…

A web server to predict the host spots in RNA binding proteins (RBPs). The method for hot spot prediction could be effectively used to narrow down the target residues for inhibiting protein–RNA…

Desktop app
practip practip

practip

A prediction method for residue-base contacts between proteins and RNAs using…

A prediction method for residue-base contacts between proteins and RNAs using only sequence information and structural information predicted from only sequences. practip can be applied to any…

Web app
RPISeq RPISeq

RPISeq

A family of classifiers for predicting RNA-protein interactions using only…

A family of classifiers for predicting RNA-protein interactions using only sequence information. Given the sequences of an RNA and a protein as input, RPIseq predicts whether or not the RNA-protein…

Desktop app
Web app
A A A lncPro lncPro

lncPro

A web app for predicting the interaction between long noncoding RNAs and…

A web app for predicting the interaction between long noncoding RNAs and proteins. By coding RNA and protein sequences into vectors, a matrix multiplication is used to give score to each RNA-protein…

Desktop app
Web app
SPOT-Struct-RNA SPOT-Struct-RNA

SPOT-Struct-RNA

RNA-binding Protein Prediction from 3D structure. This method achieves 98%…

RNA-binding Protein Prediction from 3D structure. This method achieves 98% accuracy and 91% precision for predicting RBPs and 93% accuracy and 78% precision for predicting RNA-binding amino-acid…

Web app
Protein-RNA interface Protein-RNA interface

PRince Protein-RNA interface

Analyzes the structural features and physicochemical properties of the…

Analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA…

Web app
RNA Binding score RNA Binding score

RBscore RNA Binding score

A general binding score for predicting the nucleic acid binding probability in…

A general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue…

Web app
RNABindR RNABindR

RNABindR

Identifies and displays RNA-binding residues in known protein-RNA complexes and…

Identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to identify which amino…

Telomeric Proteins… Telomeric Proteins Interaction Network

TeloPIN Telomeric Proteins Interaction Network

A database that points to provide comprehensive information on protein-protein,…

A database that points to provide comprehensive information on protein-protein, protein-DNA and protein-RNA interaction of telomeres. TeloPIN database contains four types of interaction data,…

Web app
RPI-Pred RPI-Pred

RPI-Pred

A RNA-protein interaction prediction server based on Support Vector Machine…

A RNA-protein interaction prediction server based on Support Vector Machine (SVM). The RPI-Pred uses primary sequence and predicted structural fragments information of given protein and RNA. The…

Web app
bioCOmplexes COntact… bioCOmplexes COntact MAPS

COCOMAPS bioCOmplexes COntact MAPS

A web application to easily and effectively analyse and visualize the interface…

A web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of…

Web app
CONSensun COCOMAPS CONSensun COCOMAPS

CONS-COCOMAPS CONSensun COCOMAPS

A tool to easily measure and visualize the consensus in multiple docking…

A tool to easily measure and visualize the consensus in multiple docking solutions. It uses the conservation of inter-residue contacts as an estimate of the similarity between different docking…

A A A RNA Bricks RNA Bricks

RNA Bricks

Stores information about recurrent RNA 3D motifs and their interactions, found…

Stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein complexes. Besides, the search utility enables searching…

Web app
A A A catRAPID omics catRAPID omics

catRAPID omics

A server for large-scale calculations of protein-RNA interactions. catRAPID…

A server for large-scale calculations of protein-RNA interactions. catRAPID omics allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size…

Web app
aaRNA aaRNA

aaRNA

An RNA binding site predictor using various features that out-performs…

An RNA binding site predictor using various features that out-performs sequence- or structure-only predictors.

Web app
CAD-score CAD-score

CAD-score

Contact area-based comparison of structures and interfaces of proteins, nucleic…

Contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

Web app
Web 3DNA Web 3DNA

w3DNA Web 3DNA

A user-friendly web-based interface to the 3DNA suite of programs for the…

A user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their…

Desktop app
ITScore-PR ITScore-PR

ITScore-PR

A knowledge-based scoring function for protein-RNA binding mode prediction by…

A knowledge-based scoring function for protein-RNA binding mode prediction by using a statistical mechanics-based iterative method.

Web app
KYG KYG

KYG

RNA interface residue prediction from protein 3D structure.

RNA interface residue prediction from protein 3D structure.

Web app
DR_bind1 DR_bind1

DR_bind1

This server can be used to predict the DNA-binding residues for a given protein…

This server can be used to predict the DNA-binding residues for a given protein chain.

Web app
Prediction of Protein… Prediction of Protein RNA-Interaction

Pprint Prediction of Protein RNA-Interaction

A web-server for predicting RNA-binding residues of a protein. The prediction…

A web-server for predicting RNA-binding residues of a protein. The prediction is done by SVM model trained on PSSM profile generated by PSI-BLAST search of 'nr' protein database. The SVM…

Web app
Prediction of… Prediction of RNA-binding Residues

PRBR Prediction of RNA-binding Residues

A method for identifying RNA-binding residues from amino acid sequences. PRBR…

A method for identifying RNA-binding residues from amino acid sequences. PRBR combines a hybrid feature with the enriched random forest (ERF) algorithm. The hybrid feature is composed of predicted…

Protein-DNA Interface… Protein-DNA Interface database

PDIdb Protein-DNA Interface database

A repository containing relevant structural information of Protein-DNA…

A repository containing relevant structural information of Protein-DNA complexes solved by X-Ray cristallography and available at the Protein Data Bank (PDB).

Web app
RNABindRPlus RNABindRPlus

RNABindRPlus

Protein-RNA interactions are central to essential cellular processes such as…

Protein-RNA interactions are central to essential cellular processes such as protein synthesis and regulation of gene expression and play roles in human infectious and genetic diseases. RNABindRPlus…

Biological… Biological Interaction database for…
Nucleic Acid Database Nucleic Acid Database

NDB Nucleic Acid Database

A web portal providing access to information about 3D nucleic acid structures…

A web portal providing access to information about 3D nucleic acid structures and their complexes.

Nucleic acid-Protein… Nucleic acid-Protein Interaction DataBase

NPIDB Nucleic acid-Protein Interaction DataBase

Contains structural information about all DNA–protein and RNA-protein…

Contains structural information about all DNA–protein and RNA-protein complexes available from PDB. We updated NPIDB, adding a new classification of DNA–protein complexes and their families.…

Protein-RNA Interface… Protein-RNA Interface Database

PRIDB Protein-RNA Interface Database

A comprehensive collection of all protein-RNA complexes from the Protein Data…

A comprehensive collection of all protein-RNA complexes from the Protein Data Bank (PDB).

RsiteDB RsiteDB

RsiteDB

A database and an on-line search engine, which store and query the protein…

A database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases.

A A A NPInter NPInter

NPInter

Integrates experimentally verified functional interactions between noncoding…

Integrates experimentally verified functional interactions between noncoding RNAs (excluding tRNAs and rRNAs) and other biomolecules (proteins, RNAs and genomic DNAs). Extensive studies on ncRNA…

Web app
SVM-Prot Deprecated SVM-Prot

SVM-Prot

A web app for the prediction of RNA-binding proteins directly from their…

A web app for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to…

Web app
catRAPID signature catRAPID signature

catRAPID signature

Predicts ribonucleoproteins and RNA-binding regions using physico-chemical…

Predicts ribonucleoproteins and RNA-binding regions using physico-chemical properties instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms,…

Web app
RNA-Binding Residue… RNA-Binding Residue Detector

RBRDetector RNA-Binding Residue Detector

A structure-based algorithm to identify RNA-binding residues by combining…

A structure-based algorithm to identify RNA-binding residues by combining feature- and template-based prediction strategies. Based on the well-designed evolutionary and structural features, we…

Web app
Sequence-based… Sequence-based Nucleic acid-Binding Residue Finder

SNBRFinder Sequence-based Nucleic acid-Binding Residue Finder

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues.…

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues. To address this problem, the profile HMM alignment was ingeniously utilized to establish the sequence-based template…

Desktop app
PRIPU PRIPU

PRIPU

Employs biased-support vector machine (SVM) for predicting protein-RNA…

Employs biased-support vector machine (SVM) for predicting protein-RNA interactions (PRIs) using only positive and unlabeled examples. This is the first work that predicts PRIs using only positive…

Desktop app
Web app
SPOT-Seq-RNA SPOT-Seq-RNA

SPOT-Seq-RNA

A sequence-based technique dedicated for predicting complex structures of…

A sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly…

Web app
PRINTR Deprecated PRINTR

PRINTR

A method for the prediction of protein residues that interact with RNA using…

A method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the…

Web app
Protein-RNA Deprecated Protein-RNA

PiRaNhA Protein-RNA

Predicts the location of RNA-binding residues (RBRs) in protein sequences. The…

Predicts the location of RNA-binding residues (RBRs) in protein sequences. The goal of functional annotation of sequences in the field of RNA binding is to provide predictions of high accuracy that…

Web app
RNA-interaction site… Deprecated RNA-interaction site prediction

RISP RNA-interaction site prediction

A hybrid RISP method using support vector machine (SVM) in conjunction with…

A hybrid RISP method using support vector machine (SVM) in conjunction with evolutionary information of amino acid sequences in terms of their position-specific scoring matrices (PSSMs) for…

Web app
NAPS Deprecated NAPS

NAPS

A method for the identification of amino acid residues involved in DNA- and…

A method for the identification of amino acid residues involved in DNA- and RNA-binding using sequence-based attributes. NAPS used in this work combines the C4.5 algorithm with bootstrap aggregation…

Web app
BindN BindN

BindN

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding…

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding residues from sequence features, including the side chain pKa value, hydrophobicity index and molecular mass of an amino…

Web app
BindN+ BindN+

BindN+

An upgraded version of BindN, applies support vector machines (SVMs) to…

An upgraded version of BindN, applies support vector machines (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information.

Web app
dRNA-3D Deprecated dRNA-3D

dRNA-3D

A method to predict RBPs and binding sites simultaneously based on a similar,…

A method to predict RBPs and binding sites simultaneously based on a similar, successful approach employed for predicting protein–DNA binding proteins with structural alignment to known complex…

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