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Abstract:
Background
Structural models determined by X-ray crystallography play a central role in
understanding protein-protein interactions at the molecular level.
Interpretation of these models requires the distinction between non-specific
crystal packing contacts and biologically relevant interactions. This has been
investigated previously and classification approaches have been proposed.
However, less attention has been devoted to distinguishing different types of
biological interactions. These interactions are classified as obligate and
non-obligate according to the effect of the complex formation on the stability
of the protomers. So far no automatic classification methods for distinguishing
obligate, non-obligate and crystal packing interactions have been made
available.
Results
Six interface properties have been investigated on a dataset of 243 protein
interactions. The six properties have been combined using a support vector
machine algorithm, resulting in NOXclass, a classifier for distinguishing
obligate, non-obligate and crystal packing interactions. We achieve an accuracy
of 91.8% for the classification of these three types of interactions using a
leave-one-out cross-validation procedure.
Conclusion
NOXclass allows the interpretation and analysis of protein quaternary
structures. In particular, it generates testable hypotheses regarding the
nature of protein-protein interactions, when experimental results are not
available. We expect this server will benefit the users of protein structural
models, as well as protein crystallographers and NMR spectroscopists. A web
server based on the method and the datasets used in this study are available at
http://noxclass.bioinf.mpi-inf.mpg.de/.
