Introduction to the PDB

1. RCSB
Protein
Data
Bank
1
Founded in 1998
Rutgers, The State University of
New Jersey
• Data deposition & annotation
UC San Diego,
San Diego Supercomputer Center
• Data dissemination (rcsb.org)
Query, analysis, visualization,
web services, data download

2. wwPDB
2
Wellcome Trust,
EU,
CCP4, BBSRC,
MRC, EMBL
NLM BIRD-JST, MEXT
NSF, NIGMS, DOE,
NLM, NCI,
NINDS, NIDDK
wwPDB formed in 2003
• Defines data and validation standards
• Collects, annotates, validates and disseminates PDB data

3. RCSB
PDB
West
Team
§ Science: structural and
computational biology,
structural bioinformatics,
chemoinformatics, genomics,
drug design, scientific software
development, research grants
§ Software: web design, user
experience design, database
design, web services, big data,
open source development
§ Systems: hardware,
networking, virtualization, cloud
computing, data management
3
Scientists, software engineers,
postdocs, students

4. 4

5. Growing
User
Base

6. Open
Source
Software
Development
§ BioJava
(Sequence
and
Structure
modules)
§ https://github.com/biojava
§ RCSB
PDB
SpeciNic
Software
§ https://github.com/rcsb
§ Macromolecular
Transmission
Format
(MMTF)
§ http://mmtf.rcsb.org
6