April 9, 2024

3D Science Visualization

Instructor: Bongsup Cho, PhD, University of Rhode Island

Location: URI   
Session 1: June 29-July 1 (Avedisian Hall Room 205)
Session 2: July 13-15 (Avedisian Hall Room 205)

Course Overview

This WDT Module aims to train students in modern methods of 3D science visualization. The module will include lectures and hands-on experience in molecular modeling, 3D molecule printing, protein and DNA structure prediction using the AI-based machine learning algorithm AlphaFold, Tour of Human Cell, membrabe trasporters, and the BioRender Science Illustration app. The module will provide sufficient background for students to understand and appreciate how scientists could benefit from the available state-of-the-art 3D visualization software and tools to enhance their scientific data and disseminate it with impact. The module will be completed over 2.5 days, and participants who complete it will receive an RI-INBRE Certificate of Completion.

 

Learning Outcomes

    • Navigate molecular structure databases such as the RCSB Protein Data Bank (PDB): Opioid Receptor as an example (4dkl)
    • Visualize the molecular mechanisms of RNA-based antibiotics and cancer drugs using modeling
    • Get hands-on with processing molecular structures in visualization software such as ChimeraX
    • 3D-Print your molecular models
    • Explore DNA structures and hands-on modeling of the origin of double helical structures
    • Tour of Human Cell and demo
    • Closer inspection of phospholipid transmembrane-bound ion channels and their structures and functions (Aquaporin, K+ Channel, and Na+ Channel)
    • Hands-on practice on predicting protein structures from sequence using the Nobel prize-winning machine learning algorithm AlphaFold (Chris Hemme)
      • Demo of “BioRender” Scientific Image and Illustration Visualization Software (Chris Hemme)
      • Reflection on scientists/artists’ interdisciplinary collaboration

Lab Report

Students will be expected to maintain detailed laboratory notes to include:

  • Structures analyzed and their relevance
  • 3D printing protocols, inspection of macromolecules
  • Data analysis protocols (e.g., workflows, software used, etc.)
  • Results of AlphaFold analysis

Resources Used in this Module:

  • Standard Operating Procedure – 3D Printing of Protein Structures
  • ChimeraX – 3D structure visualization of PDB files
  • Slide Decks for lectures
  • BioRender Image and Illustration Software
  • “3D Molecular Designs” Kits (DNA, Ion Channels, Phospholipid membrane models)
  • Illustration of a Human Cell

Proposed Timeline (subject to change)

 

DDay 1Day 2Day 3
9:00 AM – 10:00 AMIntroduction to Molecular Visualization and Structural Databases (Lecture)Protein structures prediction using AlphaFold (Lecture/Hands-on)
10:00 AM – 11:00 AMTour of Model Showcase
Tour of a Human Cell		Protein structures prediction using AlphaFold (Hands-on)3D Printing Chimera (continues)
11:00 AM – 12:00 PMAntiobiotics action and resistance (Hands-on)Demo of BioRender (Scientific image and illustration software)Reflections
12:00 PM – 1:00 PMBreakBreakCertificate Distribution
1:00 PM – 2:00 PM3D Projection of drug actions (Hands-on)Let’s play. Modeling of DNA structures and the origin of double helical structures (Hands-on)
2:00 PM – 3:00 PMChimeraX Prep of 3D molecule printing (Hands-on)DNA structure…continues. Modeling of phospholipid transmembrane (Hands-on)
3:00 PM – 4:00 PMChimeraX Prep of 3D molecule printing (Hands-on)DNA structure…continues. Modeling of phospholipid transmembrane (Hands-on)