Conference Proceedings

Protein topology classification using two-stage support vector machines.

Jayavardhana Gubbi, Alistair Shilton, Michael Parker, Marimuthu Palaniswami

Genome Inform | Published : 2006


The determination of the first 3-D model of a protein from its sequence alone is a non-trivial problem. The first 3-D model is the key to the molecular replacement method of solving phase problem in x-ray crystallography. If the sequence identity is more than 30%, homology modelling can be used to determine the correct topology (as defined by CATH) or fold (as defined by SCOP). If the sequence identity is less than 25%, however, the task is very challenging. In this paper we address the topology classification of proteins with sequence identity of less than 25%. The input information to the system is amino acid sequence, the predicted secondary structure and the predicted real value relative..

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