title: PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms.
abstract: 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 C(alpha) coordinates. We introduce four certain relations between C(alpha) three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: alpha-helix, 3(10)-helix, pi-helix and beta-strand. In our approach, the deviation of the C(alpha) 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.
authors.affiliation: Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
authors.forename: Sayed-Rzgar
authors.initials: SR
authors.lastname: Hosseini
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
authors.forename: Hamid
authors.initials: H
authors.lastname: Pezeshk
authors.forename: Changiz
authors.initials: C
authors.lastname: Eslahchi
authors.forename: Mahnaz
authors.initials: M
authors.lastname: Habibi
mesh_terms: D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins