Learning About Structures Using the RCSB PDB

Learning About Structures Using the RCSB PDB Wolfgang Bluhm, Production Manager The RCSB PDB at the University of California, San Diego www.pdb.org info@rcsb.org

Workshop Format • Brief introduction • Short demo • Choice of three tutorials: • Tutorial 1 (ferritin) – interactive version • Tutorial 1 (ferritin) – live Web site • Tutorial 2 (1 of 15 molecules) – live Web site

Production Web Sitewww.pdb.org or www.rcsb.org • Built on PDB files • Perl/CGI, multiple databases

Data Uniformity • Resolved… …sequence anomalies relative to SwissProt, GenBank …discrepancies between sequence and atom numbering …problems with atom naming …errors in chirality • Standardized ligand names • Described biological assemblies Nucleic Acids Res.29, 214-218, 2001 Nucleic Acids Res.30, 245-248, 2002

Curated Data • Curated data files available in… …mmCIF format on all Web and FTP sites, e.g.: ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/mmCIF/ …beta XML format on all Web sites and beta FTP site: ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML • Curated data not used for query interface of production Web sites

Reengineered Web Sitepdbbeta.rcsb.org • Built on curated data • Three-tier architecture • Database tier • Middle tier • Presentation tier • Feedback from users • Help desk • Usability engineering • Focus groups • Went into public beta testing in July 2004

RCSB PDB Team Members RCSB PDB Project Leaders: Helen M. Berman1, Philip E. Bourne2, Judith L. Flippen-Anderson1, Gary Gilliland3, John Westbrook1. RCSB PDB Project Team: Kyle Burkhardt1, Li Chen1, Sharon Cousin1, Jim Croker1, Shuchismita Dutta1, Zukang Feng1, Lew-Christiane Fernandez1, Rachel Kramer Green1, Vladimir Guranovic1, Shri Jain1, Irina Persikova1, Suzanne Richman1, Melcoir Rosas1, Bohdan Schneider1, Susan Van Arnum1, Alice Xenachis1, Huanwang Yang1, Jasmin Yang1, Christine Zardecki1, Ken Addess2, Wolfgang F. Bluhm2, Nita Deshpande2, Ann Kagehiro2, Charles Knezevich2, Jeff Merino-Ott2, Wayne Townsend-Merino2, Cindy (Qing) Zhang2, Kevin Lwinmoe3, Kathryn Rosecrans3, Elizabeth Walker3. RCSB PDB Institutions:(1) Rutgers, the State University of New Jersey, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854-8087 (2) San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093-0537 (3) Center for Advanced Research in Biotechnology / UMBI / NIST, Rockville, MD 20850

Acknowledgements • The RCSB PDB is supported by funds from • National Science Foundation (NSF) • National Institute of General Medical Sciences (NIGMS) • Office of Science, Department of Energy (DOE) • National Library of Medicine (NLM) • National Cancer Institute (NCI) • National Center for Research Resources (NCRR) • National Institute of Biomedical Imaging and Bioengineering (NIBIB) • National Institute of Neurological Disorders and Stroke (NINDS) • The worldwide PDB (wwPDB) is a collaboration of • RCSB • MSD/EBI • PDBj

Short Demo of Reengineered Web Site

Choice of 3 Tutorials • Tutorial 1: ferritin – interactive versionhttp://pdb-linux-5.rutgers.edu:8080/test/tutorials • Tutorial 1: ferritin – live Web sitehttp://pdbbeta.rcsb.org and handouts • Tutorial 2: 1 of 15 molecules – live Web sitehttp://pdbbeta.rcsb.organd handouts

Molecules (Tutorial 2)

Learning About Structures Using the RCSB PDB