The Supersized Science podcast features research and discoveries nationwide enabled by advanced computing technology and expertise at the Texas Advanced Computing Center of the University of Texas at Austin. 

The key to understanding proteins — such as those that govern cancer, COVID-19, and other diseases — is quite simple - for scientists, anyway.  Identify their chemical structure and find which other proteins can bind to them. But there’s a catch in that the search space for proteins is enormous. 

For instance, a typical protein studied is made of 65 amino acids, and with 20 different amino acid choices at each  binding position, there are 65 to the 20th power binding combinations, a number bigger than the estimated number of atoms there are in the universe.

Joining host and TACC science writer Jorge Salazar on the podcast are Brian Coventry, a research scientist with the Institute for Protein Design, University of Washington and The Howard Hughes Medical Institute; and Nathaniel Bennett, a post-doctoral scholar at the Institute for Protein Design.

Coventry and Bennett co-authored a study published May 2023 in the journal Nature Communications. 

In it their team used deep learning methods on TACC’s Frontera supercomputer to augment existing energy-based physical models in ‘do novo’ or from-scratch computational protein design, resulting in a 10-fold increase in success rates verified in the lab for binding a designed protein with its target protein.

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Story link: https://www.tacc.utexas.edu/news/latest-news/2023/08/03/deep-learning-for-new-protein-design/

Deep Learning for New Protein Design

This podcast episode focuses on a recent XSEDE Campus Bridging Success involving a site visit.

The National Science Foundation-funded eXtreme Science and Engineering Discovery Environment (XSEDE) is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services—things like supercomputers, collections of data and new tools—to improve our planet.

XSEDE’s Campus Bridging aims to make cyberinfrastructure—whether local, regional, national, or international—feel close at hand to students, researchers, and staff. Computational systems, data and information management, advanced instruments, visualization environments, and people are all linked together by software for a sense of virtual proximity akin to accessing a peripheral device plugged into the back of a laptop.

Campus Bridging helps institutions with their computer clusters, or sets of computers that work together, by providing an open-source toolkit called Rocks for deploying, managing, upgrading, and scaling applications in parallel across the cluster. Each release of Rocks has core and optional “Rolls” that provide the operating system and other applications integral to cluster computing. So, Rocks Rolls helps institutions build an XSEDE-compatible basic cluster, or XCBC. 

Campus Bridging also offers on-site visits for software installations.  

The first of such visits took place in April at Marshall University in Huntington, West Virginia. The project involved increasing the cluster’s capabilities and enhancing system management. 


An XSEDE Campus Bridging Success Story: Installation at Marshall University

Addison Snell and Michael Feldman are joined by Chris Willard, PhD, as they discuss TACC's new supercomputer and the IBM/Cisco Watson partnership.

A New Stampede in Texas and Taking Watson to the Edge

Scientists will use the $30 million system to work on data-intensive problems in life sciences, economics and genomics.

New UT Supercomputer Stampede2 Is The Fastest On Any U.S. Campus

The Supersized Science podcast highlights research and discoveries nationwide enabled by advanced computing technology and expertise at the Texas Advanced Computing Center of the University of Texas at Austin. TACC science writer Jorge Salazar hosts Supersized Science.

Supersized Science is part of the Texas Podcast Network, brought to you by The University of Texas at Austin. Podcasts are produced by faculty members and staffers at UT Austin who work with University Communications to craft content that adheres to journalistic best practices. The University of Texas at Austin offers these podcasts at no charge. Podcasts appearing on the network and this webpage represent the views of the hosts, not of The University of Texas at Austin.

Deep Learning for New Protein Design

Supersized Science Podcast

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