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Exploring Computed Structure Models on

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 website. A Virtual Crash Course was held to inform the 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 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 - 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