This software performs 3 different tasks depending on the input parameters you provide when run it, specifically, depending on the parameter CalculationType that can take the values: surface, pdb_surfaceor distance..
- If CalculationType=surface, the software reads an input file (parameter
input_file) with a set of proteins and peptides, and calculates the surface accessibility of the atoms of the aminoacids stated in the parameterAAs(i.e. K NZ, that is, the atom NZ of the Lysines). To do that, it maps your proteins to PDB entries (using Uniprot) and looks into all the possible PDB structures, and using a JMol command, calculates and reports the surface accessibilities. - If CalculationType=pdb_surface, the software takes a list of PDB entries stated in parameter
pdb_idsand calculates and reports the surface accessiblity of the atoms of the aminoacids stated in the parameterAAs(i.e. K NE, R NE, D OD, E OG, that is, the atoms NE of K and R, the atoms OD of D and the atom OG of E). - If CalculationType=distance, the software reads an input file (parameter
input_file) with a set of proteins and peptides, and calculates the minimum distance between each of these atoms: OD1 and OD2 of D (Aspartic aCID), and atoms OE1 and OE2 of E (Glutamic Acid) and any other atom in the structure.
Based on Jmol, it calculates the surface accessibility of specific sites in a given protein
You can get the latest version of the software at: http://sealion.scripps.edu/pac/
java -jar pac-calculator-1.0.jar input_parameters.properties
The input parameter file is a simple text with a set of name-value pairs of parameters.
- For surface running mode, look at example parameter file here.
- For pdb_surface running mode, look at example parameter file here.
- For distance running mode, look at example parameter file here.
For any customization of the program, report any issue or ask any question, please contact to Salvador Martinez-Bartolome (salvador at scripps.edu)