hybridRNAbind

Help | Materials | References | Acknowledgments

hybridRNAbind webserver

hybridRNAbind provides predictions of the RNA-binding residues in the input protein sequences.

Please follow the three steps below to make predictions:

1. Upload a file with protein sequences, or paste them into text area

This webserver accepts up to 10 FASTA-formated protein sequences. See Help for details of the input.

No file chosen

2. Provide email address(optional)

Please provide your email address to be notified when results are ready(optional).

3. Predict:

Click button to launch prediction.

Help

The user should submit the protein sequence(s) in FASTA format.

The format of the input file is as follows (Here is an example of input file.)

  • Line1: >protein ID
  • Line2: protein sequence (1-letter amino acid encoding)

Each protein requires two lines and multiple proteins should be placed in consecutive lines.

Materials

    Test dataset used to evaluate hybridRNAbind:
  • Test dataset: Click here to download.

Reference

  • Zhang F, Li M, Zhang J, Kurgan L. HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins. Nucleic Acids Research. 2023 Jan 11.

Acknowledgments

We acknowledge with thanks the following software used as a part of this server:

  • DeepDISObind - prediction of protein-RNA binding regions in disordered proteins
  • NCBRPred - prediction of protein-RNA binding regions in structured proteins
  • IUPred2A - Prediction of intrinsically disordered regions and disorderd binding regions
  • PSIPRED - Prediction of secondary structure
  • ASAquick - Fast neural network-based predictor of solvent accessibility
  • HHBlits - Algorithm for homology detection by iterative HMM-HMM comparison
  • PSIBLAST - Generation of the position specific scoring matrixes (PSSMs)
  • NRDB90 - The non-redundant database for usage of PSIBLAST to generate PSSMs
  • HHsuite database - The non-redundant database for uasage of HHblits to generate HMM profiles
  • SSpro and ACCpro - Prediction of protein secondary structure and solvent accessibility respectively
  • Biopython - Protein data preprocessing