
STAMP Structural Alignment of Multiple Proteins  Version 4.2

By Robert B. Russell & Geoffrey J. Barton 
Originally published in PROTEINS: Struct. Funct. Genet., 14, 309-323, 1992

Version 4.2 Announcement:  16 April 1999
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STAMP is for the alignment and comparison of protein three-dimensional
(3D) structures.

Given a set of protein domains with a similar structure, one can use
STAMP to produce a multiple alignment and associated superimposition
based on comparison of the 3D structures.

STAMP can also be used to search for similarities between a query
structure (e.g. a newly solved structure) and a database of other
structures.

The packageprovides numerous tools for the manipulation and display of
data associated with protein 3D structural similarities, including the
ability to generate superimposed coordinate sets, averaged structures,
and postcript output via molscript (structures) and alscript
(alignments).

Source code, in addition to pre-compiled executables for IRIX, Solaris, 
OSF and Linux are available free of charge by completing the form on 
http://barton.ebi.ac.uk/

New features to Version 4.2 include:

1. Programs for merging sequence/structure alignments/superimpositions
from multiple sources.

2. Assignment of probability values after Murzin (1993, JMB, 689-694)
to assess whether an observed structural similarity implies a common
superfamily (and thus a common ancestor, and usually a common
molecular function).  Note that these probability values can reveal
homology when sequence identities are insignificant.

3. The ability to read compressed PDB and DSSP files, and to read
distr/xx formatted PDB directories.

4. Programs for converting STAMP alignments (or indeed any alignment)
to various standard formats such as CLUSTAL and MSF.

