Dear all,
Do anyone knows about a Java API I could use to calculate the available surface area of a residue based on the structure of the protein (I have a PDB file). I know that this information can be retrieved from Naccess, DSSP or other software but I would like to integrate it in a Java app. I didn't found it in BioJava. It looks like Jmol has implemented it, but I cannot see how to use it from my own classes.
thanks in advance.
Arnaud
Could you convert the dssp source code into java?
I am looking for a program that computes the solvent accessible surface area for each atom (not residue) in a protein. May you please tell me if such a program or source code exists?
Hi, I eventually dropped the DDSP conversion since the ASA calculation is now implemented in BioJava. I'm not sure to understand the meaning of an atom ASA, but you can have a look, the code is open source: https://github.com/biojava/biojava