Presentation by Prlic at BOSC2012 "BioJava Update"

1. How to use BioJava
to calculate one billion protein structure alignments at
the RCSB PDB website
Andreas Prlić

2. My Two Hats
RCSB PDB
BioJava

3. Number of released entries
www.pdb.org
Overview
Year

4. Jmol
Some of the things
you can do at the
RCSB PDB site
• Advanced queries Custom
report
• Custom reports
• Visualization
• Education section
• Comparisons across PDB, based
on sequence and 3D structure
similarities Ligand
Explorer

5. www.pdb.org
Systematic Structural Alignment
Objective: Find novel relationships
Example: Green Fluorescent
Protein
§ Nidogen-1: similar 11-stranded
§ beta-barrel and internal helices
§ 3 Å RMSD, only 9% sequence identity
§ Nidogen-1: component of basement
membrane, no chromophore
§ GFP and NID-1 may share common
ancestor

6. Open Science Grid
based on the FATCAT (rigid) algorithm
Yuzhen Ye & Adam Godzik. Flexible structure alignment by chaining aligned
fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255.
Systematic comparisons of representative
chains from 40% sequence identity clusters
22000 sequence clusters
33000 representative domains

7. Java Clients can
run anywhere
Custom Job
PDB Management
Sends out instructions
Open
to clients Science
Grid
.
Writes results
to disk
.
.

8. Initial calculation of frozen
snapshot of PDB
~170k CPU hours
on OSG
Incremental weekly updates
(~1-2 million alignments)
<1000 CPU hours
1 billion alignments
available freely at
www.rcsb.org Code www.biojava.org

9. BioJava
• Major rewrite - BioJava 3

10. BioJava 1 BioJava 3
core data model
symbols/alphabets, counts, distributions
Genome/sequencing
Mult. seq. align
Structure alignment
Modfinder
AA Properties
Protein Disorder
Hmmer3 WS
NCBI WS
Parsers: Genbank/Embl/Blast

11. Acknowledgments
RCSB PDB BioJava
• Spencer Bliven • all contributors
• Peter Rose • A.Yates, J. Jacobsen, P.
Troshin, M. Chapman, J.
• Phil Bourne Gao, C.H. Koh, S. Foisy, R.
Holland, G. Rimsa, M.
Heuer, H. Brandstaetter-
Mueller, S. Willis
RCSB PDB
Funding Google Summer of Code
Open Science Grid