How to use BioJavato calculate one billion protein structure alignments at

the RCSB PDB website

Andreas Prlić

My Two Hats

RCSB PDBBioJava

www.pdb.org

Overview N

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ies

Year

Some of the things you can do at the RCSB PDB site

• Advanced queries

• Custom reports

• Visualization

• Education section

• Comparisons across PDB, based on sequence and 3D structure similarities

Jmol

LigandExplorer

Custom report

www.pdb.org

Systematic Structural AlignmentObjective: 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

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 clusters33000 representative domains

PDBCustom Job Management

Java Clients can run anywhere

Open Science

Grid

Sends out instructionsto clients

Writes resultsto disk

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Initial calculation of frozen snapshot of PDB

~170k CPU hourson OSG

Incremental weekly updates(~1-2 million alignments)

<1000 CPU hours

Code www.biojava.org

1 billion alignmentsavailable freely at

www.rcsb.org

BioJava

• Major rewrite - BioJava 3

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

Acknowledgments

• Spencer Bliven

• Peter Rose

• Phil Bourne

• all contributors

• A. Yates, J. Jacobsen, P. Troshin, M. Chapman, J. Gao, C.H. Koh, S. Foisy, R. Holland, G. Rimsa, M. Heuer, H. Brandstaetter-Mueller, S. Willis

RCSB PDB BioJava

FundingRCSB PDBGoogle Summer of Code Open Science Grid