PyData Yerevan 2022

Visualizing and Analyzing Protein Structures with UCSF Chimera
08-12, 15:30–16:15 (Asia/Yerevan), 214W PAB

Proteins are molecules that perform various functions in living cells. All proteins are composed
of the same possible twenty amino acids, but in different combinations. Based on these
combinations, proteins have different three-dimensional structures, which ultimately form the
basis of their unique functions. A protein’s structure can be determined in the laboratory or
predicted with high accuracy using artificial intelligence programs. Understanding the structures
of proteins and the ways they interact in three-dimensional space is critical for human health.
For example, a single amino acid change in a protein can lead to disease such as cancer.
In this Tutorial, participants will learn the basics of the UCSF Chimera software to visualize and
analyze protein structures. This Tutorial will be particularly useful for individuals interested in
bioinformatics and/or structural biology. No background knowledge is necessary, though it may
help to be familiar with the classifications of amino acids (charged, polar, hydrophobic) and
levels of protein structure (primary, secondary, tertiary, quaternary). This Tutorial is code-free,
but the principles learned will be useful for similar Python-based software. Materials will be
distributed via file storage links. By end of this Tutorial, participants will learn the basic principles
of protein structure, how to retrieve atomic coordinates of an individual protein or protein
complex, and how to examine and analyze protein structures with various features of UCSF

The Tutorial will serve as a crash course on protein structural biology and the molecular
visualization software, UCSF Chimera. Conceptually, participants will learn about the 20
different amino acids, the assembly of proteins, the four levels of protein structural organization,
current methods of determining the coordinates of each atom that comprises a protein structure,
and .pdb file format which contains the atomic coordinates of a protein structure. Practically,
participants will learn the core functions of UCSF Chimera to computationally assess protein
structures, including retrieving .pdb files, adjusting representations of a protein structure,
selecting specific amino acids (residues) and displaying their side chains, measuring the
distance between two selected atoms, and comparing the backbones of two protein structures.
The acquired conceptual and practical skills will serve as an ideal introduction to structural
biology and related software utilized by researchers and educators.
Minutes 0-10: Conceptual Basics of Proteins and Their Structures
Minutes 10-15: Overview of .pdb Files, UCSF Chimera, and Structure 1 + Structure 2 in Tutorial
Minutes 15-20: Launching UCSF Chimera, Retrieving Structure 1, and Changing
Minutes 20-25: Displaying Side Chains of Specific Amino Acids
Minutes 25-30: Measuring Distance Between Two Selected Atoms
Minutes 30-35: Retrieving Structure 2, Comparing Structure 1 and Structure 2, and Calculating
Root-Mean-Square Deviation
Minutes 35-40: Recap
Minutes 40-45: Questions

Prior Knowledge Expected

No previous knowledge expected

Christopher Markosian has been a student in the MD/Ph.D. program at Rutgers New Jersey Medical School since 2019. He is currently a researcher in the Arap/Pasqualini Laboratory, which is an established group studying phage display technology for various biomedical applications. His latest work centers on a protein structure-guided approach to design a phage-based immunization strategy against COVID-19. Prior to his graduate studies, he served as an instructor at Yerevan State Medical University through the Fulbright US Student Program. He completed his undergraduate studies in Molecular Biology and Biochemistry at Rutgers University–New Brunswick in 2018.