G5_RCSB PDB_030509

RCSB PDBResearch Collaboratory for Structural Bioinformatics Protein Data Bank : 

RCSB PDBResearch Collaboratory for Structural Bioinformatics Protein Data Bank Presented by: Jessica Garcia and Monika Wolinska Bioinformatics 03-05-09

What is the PDB? : 

What is the PDB? Single world wide repository of information 3D structures of large biological molecules that include: proteins and nucleic acids Supports a website where visitors can perform simple and complex queries on the data, analyze and visualize the results Accessed by 140,000 visitors per month Scientists Students General public

PDB File Format : 

PDB File Format Unique among biological data resources Provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies X-ray crystallography – method for determining the arrangement of atoms within a crystal Nuclear magnetic resonance (NMR) spectroscopy – technique which exploits the magnetic properties of nuclei Uses macromolecular Crystallographic Information File (mmCIF) data dictionaries

PDB Organization : 

PDB Organization Rutgers, The State University of New Jersey The San Diego Supercomputer Center at the University of California, San Diego Supported by funds from: National Science Foundation (NSF) Department of Energy (DOE) National Institute of General Medical Sciences (NIGMS) National Library of Medicine (NLM) National Cancer Institute (NCI) National Institute of Neurological Disorders & Stroke (NINDS) National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK)

History : 

History 1970s Community discussions about how to establish an archive of protein structures Cold Spring Harbor meeting in protein crystallography PDB established at Brookhaven National Laboratory (October 1971; 7 structures) 1980s Number of structures increases as technology improves Community discussions about requiring depositions IUCr guidelines established Number of structures deposited increases Independent biological databases established – e.g., the NDB 1990s mmCIF project completed Structural genomics begins PDB moves to RCSB 2000s Stable systems for deposition and release in production

Benefits of Using PDB : 

Benefits of Using PDB Structure knowledge: Helps to understand how it works Helps deduce role in human health, diseases and drug development Archive available at no cost New structures are released on a weekly basis

Getting Started…the Home Page : 

Getting Started…the Home Page

Auxin Structure Hits : 

Auxin Structure Hits

Auxin Structure Summary : 

Auxin Structure Summary

Auxin Jmol Structure Display : 

Auxin Jmol Structure Display

Sequence Details : 

Sequence Details

Future and Scientific Challenges : 

Future and Scientific Challenges Future 20,000 depositions per year in 2010 Complexity will increase dramatically New methods will yield new structures Scientific Challenges Number of data files continues to increase Information content of each data file is increasing Many more very large macromolecular complexes New structure determination methods Structure genomics

Slide 14: 

Thank You!!!