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
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