Embedded Files
May 2nd 2018
May 2nd 2018
speaker: Sergey Ovchinnikov
title: a workshop on protein structure prediction with Rosetta
June 6th 2018
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
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
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
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
November 7th 2018
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
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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