Secondary structure
VADAR identifies and assigns protein secondary structure using 3 different algorithms. These three methods are then combined to create a consensus secondary structure assignment. Only 3 types of secondary structure are identified: Helices are indicated with an "H", beta-strands are indicated with a "B" and coil or unstructured regions are identified with a "C". Secondary structure assignments for each residue are listed under the column labeled SCND STRUC. The first secondary structure identification method (which appears in column 1) uses a geometric masking approach that was first described by Richards and Kundrot with slight modifications. The second method (which appears in column 2) uses backbone dihedral angles to identify secondary structure elements in a manner initially described by Levitt and Greer as well as Chou and Fasman. The third secondary structure identification method uses hydrogen bonding patterns (in association with measured dihedral angles) to identify helices, beta strands and coil regions. This third method is somewhat similar to the method originally described by Kabsch and Sander. The net result or consensus secondary structure is a weighted combination of each of the three methods. VADAR’s method of secondary structure identification generally identifies a higher fraction of secondary structure elements than the DSSP algorithm (64% helices and beta strands for VADAR versus 51% helices and beta strands for DSSP). In particular, VADAR’s secondary structure assignments appear to agree more closely with secondary structures identified by visual inspection (i.e. author assignments), by STRIDE (another secondary structure assignment algorithm) or via independent methods (i.e. NMR-based NOE methods).