Fig. 1: Representation of HIV protease (PDB code 1hiv) in 1D and 3D
Each of the representations gives rise to a different type of prediction. (1D) AA , sequence in one-letter alphabet; sec , secondary structure, with H for helix, E for strand, and blank for other (observed OBS taken from DSSP (Kabsch and Sander 1983) and predicted PHD (Rost 1996)); acc , relative solvent accessibility, with b for buried (<9% exposed), blank for intermediate (9%-25%), and e for exposed (>25%; observed: OBS = DSSP and predicted: PHD). (2D) inter-residue contact-map (for simplicity omitted, see e.g. (Rost and Sander 1996)). (3D) the trace of the protein chain in three dimensions is plotted schematically as a ribbon a-carbon trace (graph generated using the RIBBON interface in WHAT IF Vriend and Sander 1993)).
