Computational protocol: Frozen in Time: The History of Proteins

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Protocol publication

[…] The secondary structures of rProtein segments were characterized by the frequency of intramolecular hydrogen bonding of backbone atoms (IMHBBA) and by solvent accessible surface area (SSA) with the programs STRIDE (), Naccess (), and by visual inspection. IMHBBAs primarily indicate extent of backbone–backbone interactions in α-helix or β-sheet (), while the SSA shows extent of collapse from extended to globular structures (). DSSP secondary structural elements “Turn”, “Bend”, and “-” were grouped as Random Coil (RC); “Extended Strand” and “Isolated Bridge” were grouped as “Sheet”; and “α-Helix”, “310-Helix”, and “π-Helix” were grouped as “Helix”. […]

Pipeline specifications

Software tools STRIDE, Naccess
Application Protein physicochemical analysis