XRRPred - X-ray Crystallography Resolution and R-free Prediction Tool

Materials | Standalone version | References | Acknowledgments | Disclaimer | Biomine

XRRPred webserver

The XRRpred webserver predicts resolution and R-free of the X-ray structure that could be produced for a given protein sequence.

Please follow the three steps below to make predictions:

1. Upload a FASTA file for one or more proteins (up to 50 sequences in total), or paste fasta input into the text area. Use example button for an example text input.

2. Provide your e-mail address (optional)

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

3. Predict:

Click button to launch prediction.

Input

XRRPred accepts one or more proteins as input. The input protein sequences should be in the FASTA format, where for the multiple-chain proteins the chain sequences must use the same prefix in their ID (before the underscore). Example below shows properly formatted input for two proteins where proteinID1 has two chains (chainID1 and chainID2) and proteinID2 has one chain.

>proteinID1_chainID1
AMINOACIDSEQUENCE
>proteinID1_chainID2
AMINOACIDSEQUENCE
>proteinID2
AMINOACIDSEQUENCE

(Here is an example of input file)

Materials

    TRAINING and TEST dataset format:
  • Line 1: >proteinid_chainid_resolution_rfree
  • Line 2: protein sequence (1-letter amino acid encoding)

Standalone version

    Standalone version can be found using the following links:
  • Source codes: Click here
  • Docker-based predictor (preferred): Click here

References

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

Acknowledgments

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

  • IUPred - Prediction of Intrinsically Unstructured Proteins
  • ASAquick - Prediction of protein accessible surface area