Bio structure
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Bio::Structure. Why. Ad hoc scripts Code is not reusable Nothing available for structure work in Bioperl (Biopython, Biojava). It’s fun. Protein Data Bank (PDB). ~18000 structures column based format entries created by user, validated when submitting

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Bio::Structure

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Bio structure

Bio::Structure


Bio structure

Why

  • Ad hoc scripts

  • Code is not reusable

  • Nothing available for structure work in Bioperl

  • (Biopython, Biojava)

  • It’s fun

Bio::Structure


Protein data bank pdb

Protein Data Bank (PDB)

  • ~18000 structures

  • column based format

  • entries created by user, validated when submitting

  • multiple versions of PDB format

  • not all entries in same format

  • a lot of info squeezed into format

  • entry / model / chain / residue / atom

  • ‘lingua franca’

  • mmCIF (successor, but who uses it)

Bio::Structure


Example code

Example code

  • my $structio = Bio::Structure::IO->new(-file => $bpti_file, -format => 'pdb');

  • # read the structure

  • my $struc = $structio->next_structure;

  • # loop over whole structure and store CYS SG atoms

  • for my $res ($struc->residue) {# we only look at CYS residues

  • next unless($res->id =~ /^CYS/);# and we only take SG atoms

  • for my $atom ($struc->get_atoms($res)) {

  • next unless( $atom->id eq "SG");

  • push @sgatoms, $atom;

  • }

  • }

  • #

  • # loop over all SG atoms and calculate the distance between them

  • #

  • [ … ]

  • # get $atom1 and $atom2

  • my $dist = calculate_distance($atom1,$atom2);

  • printf("%-6s %s - %-6s %s %-.2f\n",

  • $struc->parent($atom1)->id, $atom1->id,

  • $struc->parent($atom2)->id, $atom2->id, $dist);

Bio::Structure


Example code cont

Example code (cont)

  • # now have a look what the annotation was in the PDB file

  • print "\nThe annotation in the PDB file\n";

  • my ($ann) = $struc->annotation->get_Annotations("ssbond");

  • my $txt = $ann->as_text;# this text starts with "Value: "

  • $txt =~ s/^Value: //;# it contains lines of 65 chars long each

  • for (my $t = 0; $t <= length($txt); $t += 65) {

  • my $line = substr ($txt,$t, 65);

  • print "$line\n";

  • }

  • Complete code can be found in the bioperl distribution in

  • examples/structure/struct_example2.pl

Bio::Structure


Output

Output

  • The measured SG-SG distances are

  • CYS-5 SG - CYS-14 SG 24.10

  • CYS-5 SG - CYS-30 SG 8.36

  • CYS-5 SG - CYS-55 SG 2.00

  • CYS-14 SG - CYS-38 SG 2.05

  • CYS-30 SG - CYS-51 SG 2.05

  • The annotation in the PDB file

  • 1 CYS 5 CYS 55

  • 2 CYS 14 CYS 38

  • 3 CYS 30 CYS 51

Bio::Structure


What s not perfect the future

What’s not perfect – the future

  • “ CA “ “CA “ (*)

  • MTRIXn

  • segID (*)

  • altloc (biopython)

  • Writing ‘old format’ PDB files

  • BOF ideas

  • (*) fixed in CVS

Bio::Structure


Thanks

Thanks

  • Bioperl mailing list for help in designing objects

  • Yan-Yuan Tseng

  • Ethan Merritt

  • Joe Krahn

  • AlgoNomics

Bio::Structure


Bio structure

[email protected] NVTechnologiepark 4B-9052 Gent-Belgiumhttp://www.algonomics.com/


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