Java Api To Calculate Accessible Surface Area

Question

[Arnaud Ceol]

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

Answer 1

[Arnaud Ceol]

Available surface area (and other useful functions) have been implemented in version 4 of the BioJava library.

Answer 2

[Arnaud Ceol]

It looks like there is nothing like a ready solution.

My final choice has been to translate to Java the part of the DSSP software that concerns accessibility. I think that Jmol developers did similar job (translating DSSP), but at the moment the accessibility was excluded from their library.

DSSP source code (C++) is avaliable online: http://swift.cmbi.ru.nl/gv/dssp/. References to DSSP:

A series of PDB related databases for everyday needs. Joosten RP, Te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend G, NAR 2010; doi: 10.1093/nar/gkq1105. (PDF).

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824.

[m.taheri]

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?

[Arnaud Ceol]

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