2018 SEMINAR ARCHIVE

April 4th 2018

speaker: Chris Bahl

title: a workshop on protein design with Rosetta

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May 2nd 2018

speaker: Sergey Ovchinnikov

title: a workshop on protein structure prediction with Rosetta

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June 6th 2018

speaker: Mohammed AlQuraishi

title: End-to-end differentiable learning of protein structure

abstract: https://www.biorxiv.org/content/early/2018/02/14/265231

speaker: Julian Mintseris

title: High-density chemical cross-linking for modeling protein interactions

abstract: Here we report advances in method development, combining orthogonal cross-linking chemistries as well as improvements in search algorithms, statistical analysis and computational cost to achieve coverage of one unique cross-linked position pair for every 7-8 amino acids at 3% false discovery rate. We demonstrate that this level of cross-linking density is sufficient to reconstruct subunit architecture without any additional structural information for the subunits. 

August 1st 2018

speaker: Radek Nowak

title: Plasticity in binding confers selectivity in ligand-induced protein degradation

abstract: We utilize a comprehensive characterization of the ligand-dependent CRBN–BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Our findings that plastic interprotein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.

speaker: Victor Ovchinnikov

title: Biomolecular simulations using a flexible-boundary solvation model

abstract: Development of a flexible solvent boundary model, which combines fine granularity near solute interfaces and coarse granularity (continuum) in the bulk solvent

September 5th 2018

speakers: Kelly Brock, Nathan Rollins

title: Using natural and synthetic sequences to identify protein structure and function

abstract: We will talk about several projects using evolutionary couplings and expand to using mutational scans to predict folding.

October 3rd 2018

speaker: Dylan Marshall

title: Manipulating and Visualizing Data with Python - a 20 minute tutorial that will blow your mind

abstract: Big data this, data science that - if you've been seeking to hop aboard the "data (insert buzzword here)" hype train, I invite you to come get up to speed with the latest and greatest in python-based data manipulation and visualization tools. I kid you not, all you need is a Google Drive account - and a laptop of course. Using the medium of Google CoLab (how we will be coding Python), you will be introduced to Pandas (tool for data manipulation) and Seaborn (tool for data visualization) in the most succinct way possible. Any remaining advocates for Excel will be vigorously debated with, and definitively vanquished, over beers afterwards.

speaker: Sergey Ovchinnikov

title: a quick intro to Rosetta and how to modify it to work with cryo-em density

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November 7th 2018

speaker: David Nannemann

title: Capturing Diversity to Improve Affinity

abstract: Hit antibodies often require affinity maturation or other optimization to tune the therapeutic properties or manufacturability of the molecule. Next Generation Sequencing of the full antibody repertoire in the sample can guide affinity maturation and/or optimization processes. I will discuss two methods which leverage NGS data and sparse screening of clonal families to identify high affinity antibodies.

speaker: Mohammed AlQuraishi

title: a tutorial on deep learning

December 5th 2018

speaker: Chris Bahl

title: Discovery and engineering of enhanced SUMO protease enzymes

abstract: https://doi.org/10.1074/jbc.RA118.004146

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