Protein functions and interactions
We have developed a new technique to predict protein (enzymatique)
function, protein-protein and
protein-chemical interactions using the signature
descriptor described in the QSAR pages.
The signature of a protein sequence (or DNA sequence) is a vector of
occurence numbers of the sequence k-mers (or k-words). To predict
protein binding pairs a new type of kernel was developed where the
signagture is a product of the signatures of both the bait (target) and
the prey (ligand). The kernel, which is used with SVM compares well
in term of accuracy/precision/sensitivity with other existing
techniques. Our method is not specific to a particular type of
experimental dataset, does not require knowledge of protein domains or
physico-chemical parameters, it just uses as input a list of sequences
and binding pairs. More information can be found in the following
papers:
- Faulon J.L., Misra M., Martin
S., Sale,
K., Sapra
R.. Genome Scale Enzyme-metabolites and Drug-Target interaction
predictions using the signature molecular descriptor, Bioinformatics
in press
2007 [PMID: 18037612 ] (link
to journal)
- Martin S.,
Brown W. M., Faulon J.L. Using
Product Kernels to Predict Protein Interactions.
In Advances in Biochemical
Engineering/Biotechnology, Eds. H. Seitz
and M. Werther, Springer-Verlag. in press, 2007 [PMID: 17922100]
- Brown W. M., Martin S., Chabarek J.P., Strauss C, Faulon J.L.
Prediction of β-Strand Packing Interactions using the Signature
Product, Journal of Molecular Modeling, in press. [PMID:
16365772]
(link to journal)
- Martin S., Roe D., Faulon J.L. Predicting
Protein-Protein Interactions using Signature Products, Bioinformatics,
21, 218-26, 2005. [PMID: 15319262]. (.pdf manuscript).
Protein-Protein
Interaction Predictor Downloads
Send reprint request or comments to:
jfaulon@sandia.gov