Protein function prediction via graph kernels.
BACKGROUND
Computational approaches to protein function prediction infer protein function by finding proteins with similar sequence, structure, surface clefts, chemical properties, amino acid motifs, interaction partners or phylogenetic profiles. We present a new approach that combines sequential, structural and chemical information into one graph model of proteins. We predict functional class membership of enzymes and non-enzymes using graph kernels and support vector machine classification on these protein graphs.


RESULTS
Our graph model, derivable from protein sequence and structure only, is competitive with vector models that require additional protein information, such as the size of surface pockets. If we include this extra information into our graph model, our classifier yields significantly higher accuracy levels than the vector models. Hyperkernels allow us to select and to optimally combine the most relevant node attributes in our protein graphs. We have laid the foundation for a protein function prediction system that integrates protein information from various sources efficiently and effectively.


BACKGROUND
More information available via www.dbs.ifi.lmu.de/Mitarbeiter/borgwardt.html.
Borgwardt
Karsten M
KM
Institute for Computer Science, Ludwig-Maximilians-University Munich Oettingenstrasss e 67, 80538 Munich, Germany. borgwardt@dbs.ifi.lmu.de
Ong
Cheng Soon
CS
Schönauer
Stefan
S
Vishwanathan
S V N
SV
Smola
Alex J
AJ
Kriegel
Hans-Peter
HP
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D015233:Models, Statistical; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
D004798:Enzymes