Motivation: The number of available protein structures still lags far behind the number of known protein sequences. This makes it important to predict which residues participate in protein-protein interactions using only sequence information. Few studies have tackled this problem until now.
Results: We applied support vector machines to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. For the first time evolutionary information was used as one of the attributes and this inclusion of evolutionary importance rankings improves the classification. Leave-one-out cross-validation experiments show that prediction accuracy reaches 64%.