Video Challenge 2023
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2023 Video Challenge for High School Students

Molecular Mechanisms of
Targeted Cancer Therapies


Tutorial 2

Finding and visualizing HIV-related protein-drug complexes

In this tutorial you will learn how to find HIV drugs and protein-drugs complexes in the Protein Data Bank and how to animate a drug binding to the enzyme's active site. The video you submit for the challenge can use the molecules highlighted in this example.

UCSF Chimera was used to animate the molecules shown in the video. If you are new to the software please watch the Tutorial 1, parts 1, 2, and 3 to obtain a basic proficiency. Also, if you are new to video editing, you might want to watch parts 4 and 5 of Tutorial 1, where the basic techniques are demonstrated using Blender and Audacity.

Although we use UCSF Chimera for the tutorial series, there are many molecular viewers that allow you to save molecular images and produce basic animations that you might want to choose for your movie. An overview of the molecular viewers is compiled here.

If you are proficient in 3D animation software (Autodesk Maya, Cinema 4D, or Blender), the following plug-ins can open PDB data files and let you crate complex animations:

  • Bioblender (works with Blender)
  • ePMV (works with 3D Studio Max, Autodesk Maya, Blender, and Cinema 4D)
  • mMaya (works with Autodesk Maya)

Although the challenge requires a visualization of two HIV-related proteins, the animation of them is not required, and you might want to use just the images of proteins and edit them together with other creative media to convey the HIV related topics in your movie.

Example video

Example video created following the techniques shown below and in Tutorial 1.

Part 1
Finding HIV related drugs and animating the attachment of the drug to the active site
Video Guide

00:00 Introduction

01:08 Using Molecule of the Month to find relevant PDB IDs

01:46 Finding FDA approved HIV Drugs on the

03:17 Finding protein-drug complexes on

04:25 Identifying biological unit and asymmetric unit

05:23 Opening biological unit

07:02 Setting up copies of the model for animation

13:18 Using MatchMaker to realign animation elements

08:27 Setting up scenes

17:34 Changing transparency of the ribbon

18:50 Improving the animation/updating a scene

Part 2

A walk-through of the reminder of the scenes in the example video
Since the reminder of the example video can be recreated using techniques from the Tutorial 1 and Part 1 of this tutorial, only a walk-through of the Chimera and Blender files is provided.