Recent research resulted in the development of several 1D protein structure descriptors. They provide an important alternative for analysis/prediction of the protein structure/function. Numerous computational methods that provide accurate prediction of these descriptors from the protein sequence were proposed; they include secondary structure1-5, secondary structure content6-9, structural class10-17, fold type18-25, relative solvent accessibility26-32, contact order and number33-37, and residue depth38. Recent work shows that the tertiary structure can be recovered from three 1D descriptors39.
We developed a server that integrates predictions of several related descriptors including structural class17, fold type23, and secondary structure content9. The knowledge of these three descriptors was applied in various areas including tertiary structure prediction40, identification of domain boundaries41, analysis of protein interactions42 and prion proteins43, discrimination of outer membrane proteins44,45, and in prediction of secondary structure46, coding and noncoding RNAs47, folding and unfolding rates48-52, folding transition-state position53, DNA-binding sites54, and enzyme proteins and their class55,56. Our server, iFC2 (Integrated prediction of Fold, Class, and Content), is the first to exploit relations between the three descriptors, which are used to develop a cross-evaluation procedure that improves their predictions. iFC2 predictions provide higher quality than the predictions of the individual methods.
The server is located at http://biomine.ece.ualberta.ca/1D/1D.html.