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). Calculation of Accessible Surface Area Accessible surface areas is a measure of the solvent exposure of individual atoms or residues (measured in square Angstroms). It corresponds to the surface area of an atom (or residue) that a water molecule can access or touch. In VADAR, the accessible surface areas (ASA) for each residue is presented under two different column headers: RES ASA (residue ASA) and FRAC ASA (fractional ASA). The data listed under the RES ASA column refers to the “residue accessible surface areas” as measured in square Angstroms. The data listed under the FRAC ASA column refers to the fractional residue accessible surface areas (a value ranging from 0 to 1.0). Exposed, exterior, random coil or hydrophilic residues typically have a large fractional accessible surface areas (>0.5), while hydrophobic, beta sheet or interior residues have a small fractional accessible surface areas (<0.2). The fractional accessible surface areas is calculated by dividing a given residue’s observed accessible surface areas by the calculated accessible surface areas for that residue in an extended Gly-Xaa-Gly tripeptide (where Xaa is the residue of interest). VADAR reports accessible surface are values both for the entire amino acid residue and for the amino acid side chains. The accessible surface areas is also calculated for charged atoms (N, O), polar (N, O, S) atoms and for non-polar atoms (C). This information can be used to calculate charged, polar and non-polar surface area. Accessible surface areas measurements/estimates are particularly useful in protein structure assessment, protein structure validation and thermodynamic calculations. The values calculated for accessible surface areas (ASA) depend critically on the selection or choice of atomic or Van der Waals radii. Different methods and different authors have advocated the use of different atomic radii. As a result, VADAR provides several choices for atomic or Van der Waals radii. Calculation of Backbone and Side Chain Torsion Angles Protein torsion angles are calculated for phi, psi, omega (which corresponds to the peptide bond) and chi1 (the first side chain torsion angle) using standard IUPAC definitions. These values are listed under four different