Software Requirements for Prime

To use Prime for homology modeling, you must install or have access to the PDB, the BLAST program and associated sequence databases, and the HMMER program and Pfam database. The required third-party programs, the BLAST database for web-based searching, and the Pfam database are provided in the download and on DVD, and are installed automatically when you install the software.

Use of PSIPRED is also highly recommended for secondary structure predictions and for GPCR modeling. PSIPRED is not available on Windows. PSIPRED is not distributed as part of the Schrödinger software package—see Installing Prime Third-Party Software and Databases on Linux for information on obtaining and installing this program on Linux.

Information on the third-party software and databases can be found at the following locations:

• BLAST: http://www.ncbi.nlm.nih.gov/blast
• HMMER: http://hmmer.wustl.edu
• Pfam: http://pfam.sanger.ac.uk
• PDB: http://www.rcsb.org/pdb
• PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/

The following topics provide installation and setup information:

Installing Local Copies of the Prime Third-Party Software and Databases

Setting Environment Variables for the Prime Third-Party Software and Databases