STAMP is a suite of programs for the comparison and alignment of protein three
dimensional structures. The suite will multiply align structures and produce
a corresponding sequence alignment with confidence values associated with each
aligned position. The software will also search a database of protein
structures to identify structurally similar proteins. The suite includes a
number of utility programs for the manipulation of protein structures.
HOME
http://code.google.com/p/bio-stamp/
DOWNLOAD
https://code.google.com/p/bio-stamp/downloads/list
INSTALL
Do
./configure && make install
You may need to be root to installed to the default location:
./configure && sudo make install
Otherwise, specify an alternate directory installation prefix:
./configure --prefix=/usr/local && make install
Or, if checked out from the source repository, then first do:
autoreconf --install
./configure && make install
If installing on Ubuntu, and the math library (libm) isn't found, do:
LDADD=-lm make
Once installed, you will want to edit the file:
$prefix/share/stamp/pdb.directories
to set the path and file pattern for your PDB files
The file format is explained here:
http://www.compbio.dundee.ac.uk/manuals/stamp.4.4/node57.html
PROTEIN DATA BANK (PDB) AND DERIVED DATA
To make use of STAMP, you will need to sync a local copy of the PDB:
stamp-update-pdb [ /usr/local/data/pdb ]
# Optionally, extract Domain definitions, Fasta sequences, and build a blast database:
stamp-update-doms [ /usr/local/data/pdb ] [ /usr/local/data/pdbdom ]
stamp-update-pdbseq [ /usr/local/data/pdbdom ] [ /usr/local/data/pdbseq ]
stamp-update-blastdb [ /usr/local/data/pdbseq ] [ /usr/local/data/blastdb/pdbseq ]
# Optionally, sync the biological unit assemblies:
stamp-update-biounit [ /usr/local/data/biounit ]
# Split biological assemblies into one file per model:
stamp-update-biounit-models [ /usr/local/data/biounit ]
You may also want to download DSSP definitions for PDB entries, e.g. :
stamp-update-dssp [ /usr/local/data/dssp ]
It is recommended to do all of the above in a crontab to remain up-to-date
Note that the script aconvert has been removed. The script bp_sreformat
from BioPerl does the same alignment format conversions.
CITE
Copyright (1997, 1998, 1999, 2010) Robert B. Russell & Geoffrey J. Barton.
All use of the WORK must cite:
R.B. Russell and G.J. Barton, "Multiple Protein Sequence Alignment From
Tertiary Structure Comparison: Assignment of Global and Residue Confidence
Levels", PROTEINS: Structure, Function, and Genetics, 14:309--323 (1992).
LICENSE
See COPYING
MANUAL
http://www.compbio.dundee.ac.uk/manuals/stamp.4.4/stamp.html
BUGS
https://code.google.com/p/bio-stamp/issues/list
SOURCE
https://code.google.com/p/bio-stamp/source/list
CONTACT
mailto:stamp@russelllab.org
http://russelllab.org