Projects

StructuralAnalysis Package

The StructuralAnalysis package is an easy to use tool for automating the analysis of structural features on protein datasets (such as RB147. It has been tested and verified to work with Ubuntu and RHEL 4.
Requirements:

• GNU wget is required for downloading the PDB files from PDB
• Perl 5.8 (installed by default in most major Linux distributions) or greater is required for running the packages required below
• For running the CX (protrusion) analysis, the CX program is required, see Pintar et. al, 2002
• For running the roughness analysis, the MSROLL program from the MSP software package is required, see MSP homepage for more information
• For running the Solid Angle analysis, the MSROLL and MSFORM programs from the MSP software package is required, see MSP homepage

The Jar package (which contains the source-code and the compiled Java classes for JRE1.4+) is downloadable from here. Please extract the zip archive into a single directory as it contains necessary perl scripts for running the executable packages.
The Javadoc-style documentation for using this package within your own Java code is available here.
The jar file can be invoked from the command line as such:

java -jar StructuralAnalysis.jar -cx -rgroup <dataset>             CX Algorithm over protein's Rgroup
java -jar StructuralAnalysis.jar -cx -alphacarbon <dataset>        CX Algorithm over protein's Alphacarbon
java -jar StructuralAnalysis.jar -cx -average <dataset>            CX Algorithm over protein's Atoms
java -jar StructuralAnalysis.jar -r <dataset>                      Surface Roughness
java -jar StructuralAnalysis.jar -a <dataset>                      Solid Angle

The program expects a dataset format similar to that of RB147 and RB109 from the RNAbindr website. It will take care of downloading the required PDB files directly from PDB.