Using KBase to access PDB Structures and Computed Structure Models
Virtual Crash Course | November 22, 2022
At this virtual course, the participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. This course was organized jointly by RCSB PDB and DOE KBase.
After watching the videos featured in this course, you will be able to:
- Import experimental protein structure data into KBase from the RCSB PDB
- Upload computed structure models of proteins from AlphaFold or RoseTTAFold into KBase
- View experimental structures and computed structure models of proteins in KBase and linking to the broader KBase data resource
- Integrate protein structure analysis into the broader genomics workflows within KBase
- Use the PDB Mol* web-native graphics viewer for exploring protein structures within KBase
Additional materials for this course are available:
- Presentation Slides
- Talk synopses and the summary of the Q and A
- Overview: PDB Data, RCSB PDB, and KBase
Click on the image below to play the video.
Introduction | Using KBase to Access Protein Structures and Models
Stephen K. Burley
Director, RCSB Protein Data Bank
KBase/RCSB PDB Crash Course Objectives
Christopher Henry
KBase, Argonne National Laboratory
Protein Candidates from Function Queries in KBase
Janaka N. Edirisinghe
KBase, Argonne National Laboratory
Accessing Experimental Structures from the PDB
Dennis Piehl
RCSB Protein Data Bank, Rutgers University
Accessing Computed Structure Models generated using AlphaFold2 or RoseTTAFold(2)
Brinda Vallat
RCSB Protein Data Bank, Rutgers University
Introduction to Mol* (MolStar) Molecular Graphics System
Shuchismita Dutta
RCSB Protein Data Bank, Rutgers University
KBase Apps for Protein Structure Data Communication and Integration with RCSB PDB
Qizhi Zhang
KBase, Argonne National Laboratory
Making the Best use of Protein Structure Data in KBase and PDB
Christopher Henry
KBase, Argonne National Laboratory
