Obtain beta sheets assigned by authors from PDB file using biojava
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Entering edit mode
6.0 years ago
m.taheri ▴ 50

Hello every body.

I am using biojava 4.1 (a bioinformatics library for java) to analyze protein structure. I use following code to get secondary structure of each residue assigned by authors from PDB file:

PDBFileParser pdbFileParser = new PDBFileParser();
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);
pdbFileParser.setFileParsingParameters(params);
Structure structure = pdbFileParser.parsePDBFile(...);

for (Group atomGroup : structure.getChainByPDB(chainId).getAtomGroups())
    if (atomGroup instanceof AminoAcid) {
        AminoAcid aminoAcid = (AminoAcid) atomGroup;
        system.out.println(aminoAcid.getSecStruc());
     }
}

The method getSecStruc() of AminoAcid object returns a hash map with just one key and value. The value is a string that can be STRAND, HELIX or null. As you know every beta sheet in the protein consists of one or more beta strands. My problem is that the above code does not give me any information about beta sheets. It is just giving me beta strands and i can not figure out which group of beta strands make a beta sheet and where are beta sheets?

Thank you.

java biojava secondary structure beta sheets • 1.4k views
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