Prime User Manual - ISP

Prime User Manual
Appendix A: Third-Party Programs
A.1 Location of Third-Party Programs
Appendix A
As well as internal and bundled software and data, Prime uses certain external third-party
programs and databases for sequence and homolog searches, protein family searches, and
secondary structure prediction. These are described under the headings in this topic.
A.1.1 BLAST/PSI-BLAST, Pfam, and the PDB
See the home pages for these programs and servers for more information:
• BLAST/PSI-BLAST
http://www.ncbi.nlm.nih.gov/blast
The BLAST version distributed with Prime is version 2.2.16. To download the BLAST
database, you should use the update_BLASTDB utility. This utility uses rsync to download
or update the database, in the correct format for use with Prime.
• HMMER/Pfam
http://pfam.sanger.ac.uk
This site has links to mirror sites that may be more convenient for downloads. You can
download the Pfam database from ftp.schrodinger.com/support/hidden/prime/
Pfam_fs.gz.
• PDB
http://www.rcsb.org/pdb/
Note that the PDB format has changed, as of August 1, 2007. You should use the
rsync_pdb utility to update your local copy of the PDB for use with Prime. Prime uses
the new format, and automatically converts files in the old format.
A.1.2 Secondary Structure Prediction
Two distinct third-party secondary structure prediction programs can be used to increase the
accuracy of, and get better results from, Prime. One of these programs (SSpro) is already
bundled with Prime. The other (PSIPRED) is highly recommended, and may be manually
installed by you, at your election, and subject to applicable license terms, if any. At the third-
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