“School of Biological”Back to Papers Home
Back to Papers of School of Biological
|Paper IPM / Biological / 13242||
The automatic assignment of secondary structure from three-dimensional atomic coordinates of proteins is an essential step for the analysis and modeling of protein structures. So different methods based on different criteria have been designed to perform this task. We introduce a new method for protein secondary structure assignment based solely on CÎ± coordinates. We introduce four certain relations between CÎ± three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: Î±-helix, 310-helix, ï¿½?-helix and Î²-strand. In our approach, the deviation of the CÎ± coordinates of each residue from each relation is calculated. Based on these deviation values, secondary structures are assigned to all residues of a protein. We show that our method agrees well with popular methods as DSSP, STRIDE and assignments in PDB files. It is shown that our method gives more information about helix geometry leading to more accurate secondary structure assignment.
Download TeX format
|back to top|