SSAP: sequential structure alignment program for protein structure comparison.

I351 sequence database. We have applied a prelim'ipary version of the R3P method in combination with the 3D profile method for the prediction of several sequences to be folded as fila barrels by sequence database searches with a number of /3la barrel profiles." Program Use and Availabllity As described above there are a large number of ways to generate a profile. The method one uses depends on the application. For fold identification , there is no absolute favorite. No profile works best in all cases, but best 'results are generally obtained with continuous profiles or an R3P profile. For structure verification, the clear choice is continuous profiles. For alignment of an identified structure with the sequence, the clear choice is the R3P method. The following programs are available from the authors. ENVIRON: Calculates area buried and fraction polar for each residue 3D-PROFILER: Reads the output file from ENVIRON and generates PROFGEN: Reads the output file from ENVIRON and generates a MAKER3P: Produces an R3P profile directly fr0m.a coordinate file ALIGNR3P: Produces a sequence-R3P profile alignment by an iterative refinement procedure PROFILESEARCH: Determines optimal alignment scores for a database of sequenccs with a 3D profile; the alignment scores are converted to 2 scores, and the output is a sorted list of sequences and alignment scores VERIFY-3D: Determines the overall 3D profile scoie for a structure and the average score in regions of sequence along the structure in a structure a discrete profile continuous profile of the structure