A very specific turn structure of a peptide can be different from the average turn basis spectrum of BeStSel. As an example, the Turn component of BeStSel describes an âaverage turnâ, reflecting the various types of turns of proteins by a single basis spectrum. Also, the structure of a peptide can be unique, which cannot be described by the basis spectra of BeStSel. In such cases, the possible side-chain spectral contributions can be distinct from that of proteins. Short peptides often have extreme amino acid composition very different from the average composition of proteins. However, it can work on peptides with the following considerations: The closest structures method can be useful in such a situation.īeStSel is optimized for proteins. In the case of some unique secondary structure composition no point or only a few points are located in the box. The advantage of the method is that the rarely populated folds located within the error of estimation that do not appear with the "closest structure" method In the most dense regions of the secondary structural space hundreds of points can be found in the box. In cases of architecture and topology the ten most populated groups are presented. The resulting table shows the frequences and percentages of the different groups in the CATH categories in the order of frequency. The hits in the box are sorted out for classes, architectures and topologies. The size of the box is determined by the RMSD of BeStSel on SP175 reference set. In other words we look up the structures in a box centered to the BeStSel result. The algorithm searches on a PDB subset with <= 90% sequential homology for all the chains having single CATH domains that lie within 1.5 × RMSD distance in each structural element from the estimated secondary structure.
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