Secondary structure assignment methods
Presented below is a short description of each method applied in 2StrucCompare. Please click the to access the references. In each reference box you will find a link to the original published work and, where available, web based resources. If you use 2StrucCompare and publish your work please cite our paper (in preparation) and each of the methods you run.DSSP
Dictionary of Secondary Structure of Proteins (DSSP) assigns eight state secondary structure using hydrogen bonds alone. DSSP defines a hydrogen bond where the bond energy is below -0.5 kcal/mol based on a Coulomb approximation of the hydrogen bond energy.Stride
The STRuctural IDEntification method (STRIDE) uses empirically derived hydrogen bond energy and phi-psi torrsion angles to assign secondary structure. Torsion angles are given propensities according to how close they are to their regions in the Ramachandran plot. STRIDE is optimised to meet the visual assignments made by crystallographers.P-SEA
P-SEA assigns secondary structure using Cα coordinates. This is achieved using a short range Cα distance mask and two angle criteria for each secondary structure.STICK: Continuous assignment based on line segments
STICK finds a set of line segments independent of external secondary structure definition, allowing the segments to be used as a novel basis for secondary structure definition. This is achieved by taking the average rise/residue along each axis to characterise the segment. This approach has the advantage that the secondary structure elements are described by a continous value and are therefore not restricted to the conventional structure classes. This behavior allows structures absent of “classic' secondary structure to be encoded as line segments that can be applied in structure comparison algorithms.TM-Align
A tool for aligning 3D protein structures.