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Related publications (22)

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Corinne Scaletta, Philippe Abdel Sayed, Nathalie Hirt-Burri, Alexis Laurent

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 degrees C) a ...

MDPI2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures

Luciano Andres Abriata

Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still unsolved even for the relatively simple case of small, soluble, globular, monomeric, two-state-folder proteins. Many articles discuss the li ...

2021

Computational design of anti-CRISPR proteins with improved inhibition potency

Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Zander Harteveld, Andreas Scheck, Wei Sun, Stéphane Rosset, Julius Valten Upmeier Zu Belzen, Yujia Wang

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, ...

NATURE PUBLISHING GROUP2020

Database Alignment with Gaussian Features

Negar Kiyavash, Osman Emre Dai

We consider the problem of aligning a pair of databases with jointly Gaussian features. We consider two algorithms, complete database alignment via MAP estimation among all possible database alignments, and partial alignment via a thresholding approach of ...

MLR Press2019

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

Stéphane Joost, Robson Jose Cesconeto

Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Us ...

2017

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

Olivier Martin, Vassily Hatzimanikatis, Jacques Rougemont, Giovanna Ambrosini, Nicolas Jean Philippe Guex, Marion Leleu, Nadine Fournier, Krisztian Homicsko, Julien Dorier, Christian Iseli, Fabrice David, Maxime Jan, Sophie Barret, Philipp Bucher, Mauro Delorenzi, Julien Racle, David Gfeller, João Pedro de Matos Rodrigues, Thomas Junier, Niklaus Johner, René Dreos, Rouayda Cavin Perier, Omid Shahmirzadi, Romain Fernand Pietro Groux, Ray Marcel Marin Florez, Somi Reddy Majjigapu, Christophe Bovigny, Marco Pagni, Julien Delafontaine, Sunil Kumar, Delphine Yvette L Grun, Philippe Jacquet, Philippe Moret, Haleh Yasrebi, Daniel Federico Hernandez Gardiol, Samuel Neuenschwander, Heinz Stockinger, Sebastian Schmidt, Lucila Aimo, Yoann Mouscaz, Sara Benmohammed, Thierry Lombardot, Patrick Roelli, Benjamin Paccaud, Linda Dib, Ioannis Xenarios, Olivier Michielin, Amos Bairoch, Thierry Sengstag, Andreas Schmid, Frederic Burdet, Aline Dousse, Madeleine Suffiotti, Nicolas Salamin, Grégoire Rossier, Daniel Schmocker, Atul Sethi, Guillaume Keller, Felipe Aristides Simao Neto, Ni Ai, Leonore Wigger, Marie Ghraichy, Saumya Gupta, Rounak Vyas, Thomas Stricker

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to t ...

Oxford University Press2016

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

Berend Smit, Kyriakos Stylianou, Matthew David Witman, Samantha Lynn Anderson

In this work we present the in silico design of metal-organic frameworks (MOFs) exhibiting 1-dimensional rod topologies. We introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type ...

Royal Soc Chemistry2016

Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs

Paolo De Los Rios, Pierre Goloubinoff, Vishal Sood, Andrija Finka

Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the ot ...

Springer2015

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