PiPreD
Register to obtain a copy of PiPreD accessory scripts and programs
If you would like to download a copy of PiPreD accessory scripts and programs, please send a email to pcrpiw -at- gmail -dot- com, briefly explaining who you are, the nature of your research, and the reasons. If your e-mail address is not an academic one (i.e. *.edu, *.ac.uk, etc.) please we aware that it might get filtered by the SPAM system.Why do I have to register?
We are happy to share our software and databases with the scientific community. However, for a number of reasons, mainly funding, we want to keep track of the number of users and usage, hence the registration requirement. Be reassured that the information provided will neither be shared nor distributed.Please read carefully
Upon registration you will be contacted with further instructions. Nonetheless, please read the following information as it explains what are the requirements needed to install and run PiPreD in your local systems.
There are two major components in PiPreD: (i) The database of iMotifs, and (ii) a set of accessory scripts and programs. PiPreD
will only run on a Linux-based system (tested both on Red Hat Enterprise 5.0 and 6.0 and CentOS 5.0 and 6.0 systems). Ideally, you
have access to a medium/large computer cluster, although PiPreD can run on a local server, and a sizable chunk of disk storage, i.e
in the order of 5-10 Gb per run.
Imotifs DB
The datase is distributed as a mysql dump, hence you will need both a mysql client and a mysql server to upload the contents of the dump. The mysqldump file contains all the information to generate the database and associated tables including indexing and cross-referencing. The distribution of mysql used by our systems is mysql Ver 14.12 Distrib 5.0.95, for redhat-linux-gnu (x86_64) downloadable from here. The interfacing between the accessory scripts and the database in done using the perl-DBI and perl-DBD libraries. Finally, PiPreD also requires local copy of the entire PDB databank, in particular the directory containing individual gzipped files of the coordinates protein structures in standard format. FTP link here
Accessory scripts and programs
The accessory scripts and programs execute all the tasks related to the structural modeling of peptides, including the extraction of anchor residues, querying the database, structural modeling of peptides and preparation of input files for Rosetta. All accessory scripts are written in perl and use standard libraries except for the perl-DBD/DBI modules shown above. There is a set of scripts designed to run PiPreD on HPC environments (preferable), in particular HPC systems that use open Sun Grid engine as scheduler. There is also a set of scripts designed to run PiPreD in a local server. The actual structural modeling of peptides is done using a program written in C++ which include standard libraries. A compiler, e.g. gcc, is required to compile this program. Finally, the final stage of PiPreD, the designing of sequences relies entirely on Rosetta software suite, and thus users will have to obtain their own licenses and install the programs separately.
The datase is distributed as a mysql dump, hence you will need both a mysql client and a mysql server to upload the contents of the dump. The mysqldump file contains all the information to generate the database and associated tables including indexing and cross-referencing. The distribution of mysql used by our systems is mysql Ver 14.12 Distrib 5.0.95, for redhat-linux-gnu (x86_64) downloadable from here. The interfacing between the accessory scripts and the database in done using the perl-DBI and perl-DBD libraries. Finally, PiPreD also requires local copy of the entire PDB databank, in particular the directory containing individual gzipped files of the coordinates protein structures in standard format. FTP link here
The accessory scripts and programs execute all the tasks related to the structural modeling of peptides, including the extraction of anchor residues, querying the database, structural modeling of peptides and preparation of input files for Rosetta. All accessory scripts are written in perl and use standard libraries except for the perl-DBD/DBI modules shown above. There is a set of scripts designed to run PiPreD on HPC environments (preferable), in particular HPC systems that use open Sun Grid engine as scheduler. There is also a set of scripts designed to run PiPreD in a local server. The actual structural modeling of peptides is done using a program written in C++ which include standard libraries. A compiler, e.g. gcc, is required to compile this program. Finally, the final stage of PiPreD, the designing of sequences relies entirely on Rosetta software suite, and thus users will have to obtain their own licenses and install the programs separately.
