Schrödinger makes available copies of the third-party databases that are used by Prime. However, these databases can also be updated directly from their respective sources by the user (or system administrators). Details on how to update your copies of the PDB, BLAST, and Pfam databases are given below.

By default third-party databases are stored in the $SCHRODINGER/thirdparty directory, and in the instructions below this directory is referred to as the thirdparty directory. If you changed the default locations by setting the SCHRODINGER_THIRDPARTY or SCHRODINGER_PDB environment variable, please substitute those directories for $SCHRODINGER/thirdparty below.

Protein Data Bank (PDB)

The RCSB (maintainer of the PDB) operates FTP and rsync servers from which users can obtain regular (weekly) updates for their own local copies of the PDB. For details on the mirroring process please see:

http://www.rcsb.org/pdb/ftpproc.final.html

We recommend using rsync over FTP for obtaining updates. Recent Linux distributions include rsync, but if necessary the rsync program (in source or binary form) can be downloaded from:

http://rsync.samba.org

Prime expects to find a copy of the PDB in the database/pdb subdirectory of the $SCHRODINGER/thirdparty directory.

Please note that only a subset of the data available from the RCSB is actually required and/or used by Prime - in particular only the PDB files corresponding to current and obsolete entries are distributed by Schrödinger. Computational models as well other data such as structure factors, mmCIF files, biological units, etc., are omitted given their substantial size.

Prime 1.2 and later include an rsync_pdb script in the $SCHRODINGER/utilities directory, and it can be used to obtain or update a copy of the PDB for use with Prime. For users of earlier Prime releases, we provide an unsupported script, rysnc_pdb.sh.

BLAST databases

Updated sequence databases for use with BLAST are provided by NCBI:

http://www.ncbi.nlm.nih.gov/BLAST/

Prime 1.2 and later include an update_BLASTDB script in the $SCHRODINGER/utilities directory, and it can be used to download, format, and install pdbaa and nr BLAST databases for use with Prime. For users of earlier Prime releases, we provide an unsupported script, update_BLASTDB.sh.

Pfam database

The Pfam database, a collection of multiple sequence alignments and hidden Markov Models for common protein domains and families, is described in detail at:

http://pfam.sanger.ac.uk/

Note: For Suite 2012 and later, the Pfam database is included in the Suite download. The instructions below are for Suite 2011 and earlier.

Prime uses this database to aid users in identifying remote homologues. In particular the pfam back-end searches the Pfam fragment library Pfam_fs for potential sequence homologues. Note, however, that while the PDB and BLAST databases are required to run Prime, the Pfam database is optional and is not required to run Prime. To obtain or update the Pfam database follow the steps discussed below.

1. Create the required directory:

mkdir -p $SCHRODINGER/thirdparty/database/pfam

2. Download the database from the Schrödinger FTP site:

ftp://ftp.schrodinger.com/support/hidden/prime/Pfam_fs.gz

3. Move Pfam_fs.gz into the newly created pfam subdirectory, and extract the compressed file with the following command:

gunzip Pfam_fs.gz

PDB, BLAST, and PFAM are third-party databases ("Third-Party Databases") and may therefore be subject to third-party license agreements and fees. We (i.e.,Schrödinger, LLC and its affiliates) have no responsibility or liability, directly or indirectly, for the Third-Party Databases or for any third-party Web sites ("Linked Sites") or for any damage or loss alleged to be caused by or in connection with use of or reliance thereon. Any warranties that we make regarding our own products and services do not apply to the Third-Party Databases or Linked Sites, or to the interaction between, or interoperability of, our products and services and the Third-Party Databases. Referrals and links to Third-Party Databases and Linked Sites do not constitute an endorsement of such Third-Party Databases or Linked Sites.