Workshop Description (Intermediate Course)

The goal of the workshop is to enable the participants to submit
and rationally evaluate results of the AlphaFold protein structure
predictions.  The class will cover the basic principles of the
structural biology of proteins, protein structure visualization
(in pymol) and protein structure prediction. The participants will
have opportunity to generate AlphaFold predictions for a protein
sequence/sequences of their choice and interpret the results
(provided these will be meaningful)

Note: Depending on interest, there might be a limit on the number
of predictions generated for workshop participants; Workshop
participants interested in generating novel AlphaFold predictions
are encouraged to provide the protein sequence(s) of interest
and a short (on or two sentences) description of each protein.


Workshop Topics

Day 1

Protein structure: The basic principles of protein structural
biology, introduction to icn3d and pymol structure viewers
and to public repositories of experiemntal and predicted protein

Day 2

Protein structure prediction: Survey of structure prediction
methods – from predictions of secondry structure and memberane
topology to SwissModel/Rosetta/AlphaFold predictions of the
full, three dimensional protein structure

Day III: Data Analysis
A. TCGAanalyze: analyze data from TCGAbiolinks pipeline
B. Differential gene expression analysis with DESeq2
C. Dimensionality reduction and clustering via Uniform Manifold Approximation and Projection (UMAP)

Technical Requirements



Dr. Lukasz Salwinski is currently an assistant researcher in the laboratory of Professor David Eisenberg who, for over a decade, has been responsible for development and maintenance of The Database of Interacting Proteins ( He received his master degree in biology at the Jagiellonian University, Krakow (Poland) and earned Ph.D. at UCLA, in the group of Professor Wayne Hubbell where he applied EPR spectroscopy to study structure of pore-forming bacterial toxins. Email:




Workshop Details

Prerequisites: LS 7A (or equivalent; CHEM 153A preferred); no programing
    experience needed.
Length: 3 days, 2.5 hrs per day
Level: Advanced
Location: Boyer Hall, 529
Seats Available: 28

Spring 2024 Dates

April 30, May 1 and 2

9:30 AM – 12:00 PM