RAPTOR is a tool for predicting recombination sites from amino acid sequence as deemed useful by the protein design algorithm SCHEMA. Unlike SCHEMA, the tool allows the user to explore structural building blocks in amino acid sequences with unknown structure. RAPTOR accepts amino acid sequences, presented in the FASTA format, and predicts a normalised SCHEMA score of each residue in the sequence.

Paste or upload your sequence below.

DATA

The SCHEMA score is defined to be

and describes, for each sequence position i, the number of contacts within the window (i-w, i+w) that would be broken if the recombination site is positioned at i. c_kl=1 if residues k and l are in within 4.5 Ĺngstrom of one another, and c_kl = 0 otherwise. w is set to 14 residues.

and the normalised score is
(where max is a constant pre-set to 637).

RAPTOR is trained on a diverse and non-redundant range of protein structures. The data set consists of 945 structures taken from the PDB. The data including the calculated and normalised SCHEMA score can be found here.

REFERENCES

Bauer, D., Bodén, M., Thier, R. and Yuan, Z. Predicting structural disruption of proteins caused by crossover. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, 2005. PDF

Bodén, M. Yuan, Z. and Bailey, T. L. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. BMC Bioinformatics. In press. PDF

Contact: mikael@itee.uq.edu.au