Question

How To Extract Secondary Structure From Pdb File ?

2

Entering edit mode

11.8 years ago

joey0214.zhong ▴ 20

how to extract secondary structure from PDB file using Biojava? I want to analysis the secondary structure, wander that can use Biojava to extract from Pdb file?

biojava pdb structure • 25k views

ADD COMMENT • link updated 11.7 years ago by andreas.prlic ▴ 290 • written 11.8 years ago by joey0214.zhong ▴ 20

score 2 · Answer 1 · 2013-02-27

2

Entering edit mode

11.8 years ago

Anuraj Nayarisseri ▴ 750

You may try Stride or PDBsum. You can input your PDBID. The server will generate the secondary structure for the same.

Stride is available here http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py

PDBsum is here http://www.ebi.ac.uk/pdbsum/

Hope this will help you

ADD COMMENT • link 11.8 years ago by Anuraj Nayarisseri ▴ 750

score 1 · Answer 2 · 2013-02-27

Just extract it from the header:

http://www.wwpdb.org/documentation/format33/sect5.html

Probably you have to write your own parser but.. otherwise, you can use DSSP and parse that output which is easier. Or Stride, as Anuraj mentioned.

Biojava apparently has something about it too: http://www.biojava.org/docs/api/org/biojava/bio/structure/secstruc/SecStruc.html

score 1 · Answer 3 · 2013-03-02

You could do something like this:



import java.util.Map;
import org.biojava.bio.structure.AminoAcid;
import org.biojava.bio.structure.Chain;
import org.biojava.bio.structure.Group;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.align.util.AtomCache;
import org.biojava.bio.structure.io.FileParsingParameters;

public class DemoShowSecStruc {
    public static void main(String[] args){

        try {
            FileParsingParameters params = new FileParsingParameters();
            params.setParseSecStruc(true);

            AtomCache cache = new AtomCache();
            cache.setFileParsingParams(params);

            Structure s = cache.getStructure("4hhb");

            for ( Chain c : s.getChains()) {
                for (Group g: c.getAtomGroups()){

                    if ( g instanceof AminoAcid ){

                        AminoAcid aa = (AminoAcid)g;

                        Map<String,String> sec = aa.getSecStruc();

                        System.out.println(c.getChainID() + " " + g.getResidueNumber() + " " + g.getPDBName() + " " + " " +sec);
                    }
                }
            }

        } catch (Exception e) {

            e.printStackTrace();
        }        
    }
}