We provide PACSY Maker program for linux, which is used for building the PACSY database. It automatically downloads the latest PDB and BMRB matching information, and synchronizes with the previous version of the PACSY database. All the related entries from the PDB, BMRB and SCOP databases are downloaded and parsed to be analyzed by PACSY Maker, which extracts temperature, pH, sequences, etc. from PDB and BMRB files. In addition, each PDB entry containing multiple structural models is split into multiple PDB files to be analyzed by STRIDE. The STRIDE(Structural Identification) program is used to calculate structural attributes such as dihedral angles, secondary structures, and residue solvent accessible area; the standalone version of STRIDE must be installed before PACSY Maker is run. Hydrophobicity is calculated from the residue solvent accessible area by PACSY Maker after STRIDE analysis. Plus, Stand-alone version of MolProbity needs to be installed on your machine and you need to check "oneline-analysis" command is executable. PACSY Maker generates a MySQL insertion script file and database SQL dump files for upload purpose. The insertion script file($PACSY_DIR/SQL/ should be modified to fit into your PACSY database account. We recommend using a text editor such as VIM to substitute USER and PASSWORD strings into your own user name and password. DON'T FORGET TO INSTALL STRIDE STANDALONE BEFORE USING PACSY MAKER!!!

[Click to download] (Build 032814)

[Flowchart of PACSY Maker. It describes how PACSY Maker program recognizes the entries to be updated and downloads to process. STRIDE program is adopted in PACSY Maker to provide structural information such as dihedral angles, secondary structures and solvent accessible surface area. Hydrophobicity is calculated using the solvent accessible surface area from STRIDE outputs. After downloading and processing steps for the updating lists, PACSY Maker generates SQL dump files and an insertion script file for MySQL server.]

PACSY Analyzer

PACSY Analyzer is designed to provide an easy graphical user interface (GUI) for using PACSY database. Even though SQL language is a powerful and standardized to handle the database, however, it is not easy for an ordinary user to learn. Thus, we understood the necessity of easy method to use the database and developed PACSY Analyzer. It provides graphical user interface that user can use mouse for selecting tables and fields to search in the window dialog. According to the one’s selection, it generates a SQL sentence to be executed for PACSY database.

[Click to download]

[We developed PACSY Analyzer program to provide an easy UI for general users who are uncomfortable with SQL language. It consists of Input Filter and Output Filter tabs for setting user requests and PACSY outputs. The outputs can be exported to comma separated file format for external use.]

Last Updated: Dec 11, 2012
By Woonghee Lee (

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