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Instructions

 

Predicting RNA Binding Residues

RNABindR v2.0 predicts RNA binding residues from protein sequences using a Support Vector Machine (SVM) classifier with a position-specific scoring matrix (PSSM) profile of a protein sequence encoded using sliding windows. RNABindR's predictions are based on observed interactions from a dataset of 198 high-resolution structures of protein-RNA complexes from the PDB. Although structural information is used to determine the actual interacting residues in a protein for training RNABindR, only the protein sequence is used as input by RNABindR for generating predictions.

Protein sequences should be submitted in FASTA format; multiple sequences can be included in a single submission. You will receive your results via e-mail; expect a wait of approximately 10 minutes per sequence submitted.

RNABindR v2.0 is necessarily dynamic, and we encourage you to check back as the software improves. Furthermore, after trying your hand at RNABindR, we welcome feedback to improve the program and its ease of use. For questions or suggestions pertaining to this website and RNABindR v2.0, please contact: rnabindr_new (at) iastate.edu

How to Interpret the Output?

Your results are returned in a plain text format. A prediction of '1' indicates that the residue is predicted to be an interface residue and a prediction of '0' means that the residue is predicted to be a non-interface residue. The prediction score tells you the probability of a residue being an interface residue. If the probability is equal to or greater than 0.5, then the residue is predicted to be an interface residue. If the probability is less than 0.5, then the residue is predicted to be a non-interface residue.