DRNApred — DNA- and RNA-binding residues predictor

References | Materials | Help | Acknowledgments | Disclaimer | Biomine

DRNApred webserver

DRNApred is a server providing sequence based prediction of DNA- and RNA-binding residues.

Please follow the three steps below to make predictions:

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

Server accepts up to 100 (FASTA formated) protein sequences. Either upload a file or enter each protein in a new line in the following text field (see Help for details):

2. Provide your e-mail address (required)

Please provide your e-mail address to be notified when results are ready.

3. Predict:

Click button to launch prediction.

References

Upon the usage the users are requested to use the following citation:

Materials

  • TRAINING dataset - Dataset used to develop DRNApred
  • TEST dataset - Dataset used to evaluate and compare DRNApred with the other existing methods. Test dataset shares low (<30%) pairwise sequence similarity with the Training dataset.
    The format of these datasets is as follow:
  • Line 1: >protein ID
  • Line 2: protein sequence (one letter amino acid code)
  • Line 3: annotation of native DNA-binding residues (1 -- DNA-binding, 0 -- nonDNA-binding, 2 -- unknown)
  • Line 4: annotation of native RNA-binding residues (1 -- RNA-binding, 0 -- nonRNA-binding, 2 -- unknown)

Help

DRNApred accepts either single or multiple protein sequences and the input is limited to 100 protein sequences at a time. The user should submit the protein sequence(s) in FASTA format.

The format of the input is as follows (EXAMPLE):

  • line1: >protein name
  • line2: protein sequence (one letter amino acid code)

Acknowledgments

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

  • HHBlits - Homology detection by iterative HMM-HMM comparison
  • IUpred - Prediction of Intrinsically Unstructured Proteins
  • PSIPRED - Protein secondary structure prediction
  • PROFphd - Protein solvent accessibility prediction
  • Rvpnet - Prediction of real valued accessibility surface area of proteins