Exploring Computed Structure Models on RCSB.org
Virtual Crash Course | September 22, 2022
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website. A Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
After watching the videos featured in this course, you will be able to:
- Understand what is a computed structure model (CSM) and how it differs from an experimental structure (PDB structure)
- Use various rcsb.org search tools to find CSMs and PDB structures
- Visualize the sequences of models and map them onto 3D structure
- Be able to assess the quality of CSMs and PDB structures
- Be able to visualize CSMs and PDB structures using web-native graphics viewer MolStar (Mol*)
Click on the image below to play the video.
Exploring Computed Structure Models on RCSB.org - Introduction
Stephen K. Burley
Director, RCSB Protein Data Bank
What is in a Computed Structure Model? Meet AlphaFold and RoseTTAFold
Brinda Vallat
Scientific Software Developer/PDB-Dev Representative and ModelCIF Manager
How do I find models? Simple Searching Case Study and intro to Structure Summary Pages
Shuchismita Dutta
Scientific Educational Development Lead and Documentation Lead
Advanced Searching, Group Summary Pages, and 1D-3D Tool
Joan Segura
Scientific Software Developer, RCSB PDB/UCSD
Computed Structure Models: Confidence Levels in 3D Predictions
Chenghua Shao
Scientific Software Developer/KPI Evaluator, RCSB PDB/Rutgers
Computed Structure Models: Visualization, Validation, and Alignments
Sebastian Bittrich
Scientific Software Developer, RCSB PDB/UCSD
