Announcements

Theme analysis is due tonight
Selected papers are also on perusall
I will be releasing L03 pre-class assignment tonight or tomorrow
- You can start reading the paper beforehand
- I do not expect you to come to lecture understanding most of the paper

The theme/primer is a starting point, not a limitation

Protein structure prediction

CADD

Requirement: Must compare and contrast various protein structure prediction methods

Requirement: Must be related to protein-ligand docking and/or molecular simulations

You could focus on ...

Antibody-antigen binding
Enzyme design
Drug targets

You could focus on ...

ML vs physics-based scoring functions
Cost or accuracy of alchemical simulations
Rigid and Flexible docking

How to find and identify specific article types

Review

Include "Review" in the search
It does not have a Materials or Methods section
Can be very, very long with tons of citations

Let's start with a basic AlphaFold search

Primary

Perspective

Has a Materials or Methods section
Look for "Research article" or "Journal article" on the article

Include "perspective OR opinion" in the search
Similar to Reviews, the authors can add their opinions instead of being solely based on literature

Your professional growth is my goal

Each activity is designed to improve your readiness for higher education or employment

However, I may over or under estimate required effort or time

Please let me know if an activity or assignment is too much; I can be flexible within reason

After today, you should be able to

1. Identify the main question, hypothesis or innovation, and significance.
2. Evaluate and understand the methods.
3. Interpret figures, tables, and data visualizations.
4. Identify the key takeaways and conclusions.
5. Apply critical thinking skills to assess the strengths, limitations, and biases.

Today's paper

Link

We are going to learn and practice effective reading techniques for an unfamiliar research article

General outline for each section:

Guided reading
Group discussions
Alex fills in any gaps and explanations

Introduction Activity

After today, you should be able to

1. Identify the main question, hypothesis or innovation, and significance.
2. Evaluate and understand the methods.
3. Interpret figures, tables, and data visualizations.
4. Identify the key takeaways and conclusions.
5. Apply critical thinking skills to assess the strengths, limitations, and biases.

Method Activity

Ten-minute break

After today, you should be able to

1. Identify the main question, hypothesis or innovation, and significance.
2. Evaluate and understand the methods.
3. Interpret figures, tables, and data visualizations.
4. Identify the key takeaways and conclusions.
5. Apply critical thinking skills to assess the strengths, limitations, and biases.

Data Activity

After today, you should be able to

1. Identify the main question, hypothesis or innovation, and significance.
2. Evaluate and understand the methods.
3. Interpret figures, tables, and data visualizations.
4. Identify the key takeaways and conclusions.
5. Apply critical thinking skills to assess the strengths, limitations, and biases.

Results Activity

After today, you should be able to

1. Identify the main question, hypothesis or innovation, and significance.
2. Evaluate and understand the methods.
3. Interpret figures, tables, and data visualizations.
4. Identify the key takeaways and conclusions.
5. Apply critical thinking skills to assess the strengths, limitations, and biases.