PIBASE
Queries (detailed) | Introduction | Statistics | Download | related work

There are two ways to install PIBASE locally: (1) download the latest compiled database , or (2) download the software package and build your own version. The first is documented and doesnt require any compute power, the second is minimally documented and requires a computing cluster or a lot of patience. The installation process is described here: pibase_installation_guide.pdf

Downloading PIBASE
PIBASE is made available under the GPL license.

The PIBASE database is composed of a mysql database and compressed text files stored on disk. You probably do not need all of the compressed files for your purposes. Read the installation guide for details on what to download. For example, for mysql queries, all you need is the mysql dump. For a web server, you would also need the software package, the domain structure files, and the complex interaction topology graphs.

software
PIBASE software package (14 MB)
mysql data
PIBASE mysql dump (225 MB)
tables on disk
Residue listing for each structure (547 MB)
Secondary structure assignment for each structure (302 MB)
Contacts between residues in each binding site (2.4 GB)
Contacts between secondary structure elements in each binding site (415 MB)
Contacts between residues across each interface (749 MB)
"Special" contacts between residues across each interface (eg H-bonds,SS-bridges) (118 MB)
Contacts between basic secondary structure elements across each interface (184 MB)
Contacts between detailed secondary structure elements across each interface (189 MB)
Secondary structure content at each interface (1.4 GB)
Residues in each patch (spatially contiguous subsets of binding sites) (238 MB)
Residue listing for each domain (560 MB)
webserver required files
Complex interaction topology graphs (500 MB)
Domain structure files (18.7 GB)

Installing PIBASE locally
The installation process is described here: pibase_installation_guide.pdf

Installing the compiled version is very simple and fast. Alternatively, you can build the database yourself locally. If you choose to do this, a cluster is necessary: it takes about 5 days to build the database on 75x AMD x86-64 nodes. The documentation for this process is minimal, but slowly being improved. The build process consists of editing a config file to specify your directory structure and mysql database specs and then basically running perl scripts/build_pibase.pl.
Essentially everything is automatic, you just need to have a local PDB (and PQS, if you wish) repository. The program automatically retrieves all other external data sources, processes them, performs all computations, and imports the results into the mysql database; using an SGE cluster if you have it available.


davisf at janelia dot hhmi dot org