Based on Jmol, it calculates the surface accessibility of specific sites in a given protein. Optionally it measures the distances between specific atoms of specific sites in the structure of the protein
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README.md

ProteinAccessibilityCalculator (PAC)

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 parameter AAs (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_ids and calculates and reports the surface accessiblity of the atoms of the aminoacids stated in the parameter AAs (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

How to get the software

You can get the latest version of the software at: http://sealion.scripps.edu/pac/

How to run it

java -jar pac-calculator-1.0.jar input_parameters.properties

Parameters files

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.

Getting help

For any customization of the program, report any issue or ask any question, please contact to Salvador Martinez-Bartolome (salvador at scripps.edu)