Lecture

Protein Structure Analysis

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In course

BIO-212: Biological chemistry I

Biochemistry is a key discipline for the Life Sciences. Biological Chemistry I and II are two tightly interconnected courses that aim to describe and understand in molecular terms the processes that make life possible. ...

Description

This lecture covers the analysis of protein structures using PyMOL software, focusing on commands, screen settings, and selection of residues. It also delves into the visualization of amino acid sequences, atoms, and residues, as well as the color coding and selection of protein structures.

Instructors (4)

Matteo Dal Peraro

Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007. His research at the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.

Bruno Emanuel Ferreira De Sousa Correia

Throughout my PhD and postdoctoral studies I was trained in world-renowned laboratories and institutions in the United States of America (University of Washington and The Scripps Research Institute). Very early in my scientific career I found out my fascination about protein structure and function. My PhD studies evolved in the direction of immunogen design and vaccine engineering which sparked my interest in the many needs and opportunities in vaccinology and translational research. My efforts resulted in an enlightening piece of work where for the first time, computationally designed immunogens elicited potent neutralizing antibodies. During my postdoctoral studies I joined a chemical biology laboratory at the Scripps Research Institute. In this stage I developed novel chemoproteomics methods for the identification of protein-small molecule interaction sites in complex proteomes. In March 2015, I joined the École Polytechnique Fédérale de Lausanne (EPFL) – Switzerland as a tenure track assistant professor. The focus of my research group is to develop computational tools for protein design with particular emphasis in applying these strategies to immunoengineering (e.g. vaccine and cancer immunotherapy). The activities in my laboratory focus on computational design methods development and experimental characterization of the designed proteins. Our laboratory has been awarded with 2 prestigious research grants from the European Research Council. Lastly, I have been awarded the prize for best teacher of Life sciences in 2019.

Giovanni D'Angelo

Teaching & PhD PhD Students Mélissa Ruiz, Gary Domeniconi, Irmak Kaysudu, Alessandro Valente, Surayyo Akramkhanova, Jean Andrea Maillat, Linda Wedemann, Manel Leila Nadia Boussouf, Jiayan Lin, Nika Gorsek, Christina Ulrich, William Daniel Chan-Ha Verdier Past EPFL PhD Students Laura Capolupo, Jaipreet Singh Loomba, Halima Hannah Emilie Schede Past EPFL PhD Students as codirector Muhammad Umair Anwar Courses Biological chemistry II BIO-213 Biochemistry is a key discipline in the Life Scienc

Official source

Related concepts (31)

PyMOL

PyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrodinger, LLC.

Molecular graphics

Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically.

OpenGL

OpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. The API is typically used to interact with a graphics processing unit (GPU), to achieve hardware-accelerated rendering. Silicon Graphics, Inc. (SGI) began developing OpenGL in 1991 and released it on June 30, 1992; applications use it extensively in the fields of computer-aided design (CAD), virtual reality, scientific visualization, information visualization, flight simulation, and video games.

Intel

Intel Corporation (commonly known as Intel) is an American multinational corporation and technology company headquartered in Santa Clara, California. It is one of the world's largest semiconductor chip manufacturer by revenue, and is one of the developers of the x86 series of instruction sets found in most personal computers (PCs). Incorporated in Delaware, Intel ranked No. 45 in the 2020 Fortune 500 list of the largest United States corporations by total revenue for nearly a decade, from 2007 to 2016 fiscal years.

CPU cache

A CPU cache is a hardware cache used by the central processing unit (CPU) of a computer to reduce the average cost (time or energy) to access data from the main memory. A cache is a smaller, faster memory, located closer to a processor core, which stores copies of the data from frequently used main memory locations. Most CPUs have a hierarchy of multiple cache levels (L1, L2, often L3, and rarely even L4), with different instruction-specific and data-specific caches at level 1.

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