biology/pdbalign 20030812 NetBSD

Given a GCG multiple sequence alignment file (a GCG MSF file), which a includes a sequence of known structure, the program pdbalign maps the sequence variability onto the known structure. The central premise is of course, that for a closely related family of proteins (sequence ID > 40%) the 3-D structures will not be significantly different.pdbdist calculates the distance from each atom in the pdb file to each atom in the ligand and records the minimum in the temperature field for that atom record.distalign reads the output from pdbdist and also the original GCG MSF file and produces an MSF file annotated with a measure of sequence variability and the distance of the residue at that position (of the sequence of known structure) from the ligand.