STAMP is a package for the alignment of protein sequence based on
three-dimensional (3D) structure. It provides not only multiple
alignments and the corresponding `best-fit' superimpositions, but
also a systematic and reproducible method for assessing the
quality of such alignments. It also provides a method for protein
3D structure data base scanning. In addition to structure
comparison, the STAMP package provides input for programs to
display and analyse protein sequence alignments and tertiary structures.
Please note that, although STAMP outputs a sequence alignment, it is
a program for 3D structures, and NOT sequences. If
you are after a multiple sequence alignment for proteins of unknown 3D
structure, stop reading now. Contact GJB for information
about AMPS, which can be used to perform multiple sequence
Comparison of 3D structures is a complicated business, particularly if one wants to do unusual things (i.e. reverse a strand direction, swap two segments of a structure around, only consider equivalent structures of greater than 10 residues, etc.). Complicated things are possible with STAMP but as a consequence, the method is very detailed. Please be patient, and read this manual carefully.
Alternatively, if you only want to to fairly straightforward things, such as align a set of structures or search a database of structures for similarities, you can skip this entire chapter and go straight to the next one, which contains a few worked examples that should demonstrate how to use STAMP in a black-box way.