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