Conformation properties of short oligopeptides and prediction of protein chain conformation

Motivation: Modem methods of protein secondary structure prediction, based entirely on protein sequences, have a very good results for "typical" alpha- and beta-structures. But there are no accurate prediction methods for other types of the protein chain conformation, firstly for polyproline 11 left-helical conformation (PPII). However, PPII conformation has a very important biological role. New approaches of protein chain conformation annotation are required for adequate fold recognition and modeling. Results: The different conformation type fragments in the globular proteins of the protein databank (PDB) were analyzed. We revealed the interrelation between sequence and structure even for very short oligopeptides. It was found the tetrapeptides with a good preference of distinct types of secondary structure. It is the first method for structure annotation with a relatively high accuracy level (similar to 60 %) for PPII conformation prediction. Availability: WEB-server containing tetrapetide structure properties databank and search tool: http://strand.imb.ac.ru/consol/index.html. Protein chain conformation prediction method: http://strand.imb.ac.ru/ssp/index.html.