PDBx/mmCIF crash course TEST
ersUse PDB data to their full extent: Undtanding PDBx/mmCIF
*Wednesday, May 3rd 2023 | 1:00 PM EDT
Registration:* go.rutgers.edu/u3vpwjet https://go.rutgers.edu/u3vpwjet
*
- This RCSB Protein Data Bank (PDB) virtual course will be broadcast on
Zoom. Please fill out the registration form to receive the Zoom link.
Registration will be available online from March 1, 2023 to May 3, 2023.
***LEARNING OBJECTIVES
*Understand the basics of PDBx/mmCIF data dictionary and file format
that underpin archiving of more than 200,000 experimentally determined
three-dimensional biostructures in the PDB. Learn about software tools
for generating and working with PDBx/mmCIF files, and programmatic
access for harvesting PDB data. Main topics:
- PDBx/mmCIF format description and examples
- PDBx/mmCIF data model
- Software tools for generating, editing, and visualizing PDBx/mmCIF files
- PDBx/mmCIF dictionary extensions, including ModelCIF for computed
structure models (CSM) from AI/ML - Parsing data from PDBx/mmCIF files for your research
**WHO SHOULD ATTEND
**Professionals and graduate students interested in learning about
strategies to take full advantage of PDB data in the fields of:
- Structural biology
- Cheminformatics and computational chemistry
- Bioinformatics and computational biology
*PROGRAM | Download Printable Program
https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf
1:00–1:10 PM
/Welcome/
Stephen K. Burley, M.D., D.Phil.
Director, RCSB PDB and Founding Director,
Institute for Quantitative Biomedicine, Rutgers University
1:10–1:25 PM
/*Introduction and course objectives
/Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University/
*/
1:25–1:45 PM
/*PDBx/mmCIF format - Not your parents’ legacy PDB format
*/Ezra Peisach, Ph.D., RCSB PDB, Rutgers University
1:45–2:05 PM
*/PDBx/mmCIF data files - Lifting the lid off the black box
/*Brian Hudson, Ph.D., RCSB PDB, Rutgers University
2:05–2:50 PM/**/ /*Programmatic data access and analysis using
PDBx/mmCIF files
*/Irina Persikova, Ph.D. and Chenghua Shao, Ph.D.,
RCSB PDB, Rutgers University
2:50–3:00 PM /*Closing remarks and acknowledgements
*/Stephen K. Burley, M.D., D.Phil.
wwPDB logo http://www.wwpdb.org/
Development and management of the PDBx/mmCIF data dictionary is a
collaborative effort involving RCSB PDB, Worldwide Protein Data Bank
(wwPDB, wwPDB.org http://www.wwpdb.org/) partners, and members of the
wwPDB PDBx/mmCIF Working Group (wwpdb.org/task/mmcif
https://www.wwpdb.org/task/mmcif).
CO-ORGANIZERS
*
*
RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian
Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan,
Chenghua Shao, Jasmine Young
(Rutgers, The State University of New Jersey).
QUESTIONS
*Contact Michelle Sanghera msanghera@iqb.rutgers.edu
**
*CO-SPONSORS
RCSB PDB logo https://www.rcsb.org/ IQB Logo
RCSB Protein Data Bank
**rcsb.org https://www.rcsb.org/
*Institute for Quantitative Biomedicine*
**iqb.rutgers.edu https://iqb.rutgers.edu/
RCSB PDB is managed by
RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF
RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE
(DE-SC0019749), and the NIH (R01GM133198).
RCSB PDB is a founding member of the wwPDB.
**
**
Institute for Quantitative Biomedicine (IQB) | iqb.rutgers.edu
https://iqb.rutgers.edu/
RCSB Protein Data Bank (RCSB PDB | rcsb.org https://www.rcsb.org/
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd. | Piscataway, NJ 08854-8076
Contact: Michelle Sanghera
E: msanghera@iqb.rutgers.edu
