RI-INBRE Workforce Development Training (WDT) Summer 2023 Syllabus

Module Title: 3D Science Visualization

Instructor: Bongsup Cho, PhD, and Christopher Hemme, PhD

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 printing, virtual reality, and , and protein structure prediction using machine learning algorithms. The module is intended for students new to 3D science visualization and structural methods and will provide sufficient background for students to pursue further training in these, and related research areas.

Learning Outcomes

  • Navigate molecular structure databases such as the RCSB Protein Data Bank (PDB) and PubChem
  • Visualize the molecular mechanism of antibiotics and cancer drugs in molecular modeling and 3D printing
  • Process molecular structures in visualization software such as Chimera
  • Print molecular structures using a 3D printer
  • Visualize and analyze molecular structures in virtual reality
  • Predict protein structures from sequence using the AlphaFold

Lab Report

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

  • Structures analyzed and their relevance
  • Data analysis protocols (e.g., workflows, software used, etc.)
  • Quality control metrics for sequencing and data analysis
  • Results of AlphaFold analysis

Resources Used in this Module:

  • Standard Operating Procedure – 3D Printing of Protein Structures
  • Nanome – 3D structure visualization in VR
  • Chimera/ChimeraX – 3D structure visualization
  • HTC Vive virtual reality headsets
  • Slide Decks for Lectures


 Day 1Day 2Day 3
9:00 AM-10:00 AMIntroduction to Structural Biology, Molecular Visualization, and Structural Databases (Lecture)Pre-Processing of Molecular Structures for Printing (Hands-On)Processing of 3D Printed Models (Hands-On)
10:00 AM-11:00 AMTour of Model ShowcasePre-Processing of Molecular Structures for Printing (Hands-On)Processing of 3D Printed Models (Hands-On)
11:00 AM-12:00 PMAntibiotics action and resistance (Hands-on)Nanoparticle VR Demo (Hands-On)Frontiers in Structural Biology (Discussion)
12:00 - 1:00 PMBreakBreakClosing Group Lunch
1:00 PM-2:00 PMAnticancer drug, Methotrextate (MTX)Visualizing Molecular Structures in Virtual Reality with Nanome (Hands-On)
2:00 PM-3:00 PMAnticancer drug, Methotrextate (MTX)AlphaFold Demonstration in ChimeraX (Hands-On)
3:00 PM-4:00 PMMethotrexate VR DemoAlphaFold Demonstration in ChimeraX (Hands-On)