Enzymes' power for plastics degradation

V Tournier, S Duquesne, F Guillamot… - Chemical …, 2023 - ACS Publications
Plastics are everywhere in our modern way of living, and their production keeps increasing
every year, causing major environmental concerns. Nowadays, the end-of-life management …

Engineering the third wave of biocatalysis

UT Bornscheuer, GW Huisman, RJ Kazlauskas, S Lutz… - Nature, 2012 - nature.com
Over the past ten years, scientific and technological advances have established biocatalysis
as a practical and environmentally friendly alternative to traditional metallo-and …

Fast and flexible protein design using deep graph neural networks

A Strokach, D Becerra, C Corbi-Verge, A Perez-Riba… - Cell systems, 2020 - cell.com
Protein structure and function is determined by the arrangement of the linear sequence of
amino acids in 3D space. We show that a deep graph neural network, ProteinSolver, can …

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

RMC Vernon, PA Chong, B Tsang, TH Kim, A Bah… - elife, 2018 - elifesciences.org
Protein phase separation is implicated in formation of membraneless organelles, signaling
puncta and the nuclear pore. Multivalent interactions of modular binding domains and their …

PremPS: Predicting the impact of missense mutations on protein stability

Y Chen, H Lu, N Zhang, Z Zhu, S Wang… - PLoS computational …, 2020 - journals.plos.org
Computational methods that predict protein stability changes induced by missense
mutations have made a lot of progress over the past decades. Most of the available methods …

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

R Nikam, A Kulandaisamy, K Harini… - Nucleic acids …, 2021 - academic.oup.com
ProThermDB is an updated version of the thermodynamic database for proteins and mutants
(ProTherm), which has∼ 31 500 data on protein stability, an increase of 84% from the …

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

P Leuenberger, S Ganscha, A Kahraman, V Cappelletti… - Science, 2017 - science.org
INTRODUCTION Temperature is crucially important to life. Small temperature changes can
differentiate optimal and lethal growth conditions of living organisms. Because of the higher …

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Z Cang, GW Wei - PLoS computational biology, 2017 - journals.plos.org
Although deep learning approaches have had tremendous success in image, video and
audio processing, computer vision, and speech recognition, their applications to three …

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

D Esposito, J Weile, J Shendure, LM Starita… - Genome biology, 2019 - Springer
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

[HTML][HTML] FoldX as protein engineering tool: better than random based approaches?

O Buß, J Rudat, K Ochsenreither - Computational and structural …, 2018 - Elsevier
Improving protein stability is an important goal for basic research as well as for clinical and
industrial applications but no commonly accepted and widely used strategy for efficient …