Publication

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

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This book has been designed for instructors in higher education or adult training who wish to develop a new course or revise an existing one. It adopts a practical, visual, and modular approach based on the principle of constructive alignment. At its heart ...

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Two design studios were successively taught in two schools of architecture: one at the Harvard Graduate School of Design (GSD) and the other at the Swiss Federal Institute of Technology in Lausanne (EPFL) in Lausanne, Switzerland, based on "A Global Morato ...

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Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

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Preventing the misfolding or aggregation of TDP-43 is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. In our work, we provide proof of concept that native state stabili ...

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Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

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Surface segregation in high-entropy alloys from alchemical machine learning

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High-entropy alloys (HEAs), containing several metallic elements in near-equimolar proportions, have long been of interest for their unique mechanical properties. More recently, they have emerged as a promising platform for the development of novel heterog ...

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HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology

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Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

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Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

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A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

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Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

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De novo protein design by inversion of the AlphaFold structure prediction network

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De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

A new age in protein design empowered by deep learning

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The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

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Generative power of a protein language model trained on multiple sequence alignments

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Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023