Computational Biology Seminar
(BIOSC 1630)
Sep 4, 2024
Lecture 02:
Reading literature
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
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
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.
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.
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.
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.
Kinase
Phosphorylate proteins and are popular drug targets
For example, my friend (and collaborator) works on MNK1 for cancer treatments
Molecular simulations give us physical insight into protein-ligand binding
Alchemical simulations
Replica exchange
Alchemical simulations
Envelope distribution sampling
Before the next class, you should
- Turn in theme analysis
- Turn in the L03 pre-class assignment
Lecture 03:
Paper 01
Lecture 02:
Reading literature
Today
Next Wednesday