The emerging role of mass spectrometry-based proteomics in drug discovery

F Meissner, J Geddes-McAlister, M Mann… - Nature Reviews Drug …, 2022 - nature.com
Proteins are the main targets of most drugs; however, system-wide methods to monitor
protein activity and function are still underused in drug discovery. Novel biochemical …

Ion mobility mass spectrometry (IM-MS) for structural biology: insights gained by measuring mass, charge, and collision cross section

E Christofi, P Barran - Chemical Reviews, 2023 - ACS Publications
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-
MS) techniques has provided substantial insights into the field of structural biology over the …

[HTML][HTML] Mega-scale experimental analysis of protein folding stability in biology and design

K Tsuboyama, J Dauparas, J Chen, E Laine… - Nature, 2023 - nature.com
Advances in DNA sequencing and machine learning are providing insights into protein
sequences and structures on an enormous scale. However, the energetics driving folding …

Protein representation learning by geometric structure pretraining

Z Zhang, M Xu, A Jamasb… - arXiv preprint arXiv …, 2022 - arxiv.org
Learning effective protein representations is critical in a variety of tasks in biology such as
predicting protein function or structure. Existing approaches usually pretrain protein …

Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome

N Wan, N Wang, S Yu, H Zhang, S Tang, D Wang… - Nature …, 2022 - nature.com
Lactylation was initially discovered on human histones. Given its nascence, its occurrence
on nonhistone proteins and downstream functional consequences remain elusive. Here we …

In-cell structural biology by NMR: the benefits of the atomic scale

FX Theillet - Chemical reviews, 2022 - ACS Publications
In-cell structural biology aims at extracting structural information about proteins or nucleic
acids in their native, cellular environment. This emerging field holds great promise and is …

[HTML][HTML] Fine-tuning protein language models boosts predictions across diverse tasks

R Schmirler, M Heinzinger, B Rost - Nature Communications, 2024 - nature.com
Prediction methods inputting embeddings from protein language models have reached or
even surpassed state-of-the-art performance on many protein prediction tasks. In natural …

Genetics of adaptation

K Bomblies, CL Peichel - Proceedings of the National …, 2022 - National Acad Sciences
The rediscovery of Mendel's work showing that the heredity of phenotypes is controlled by
discrete genes was followed by the reconciliation of Mendelian genetics with evolution by …

[HTML][HTML] A roadmap for metagenomic enzyme discovery

SL Robinson, J Piel, S Sunagawa - Natural Product Reports, 2021 - pubs.rsc.org
Covering: up to 2021 Metagenomics has yielded massive amounts of sequencing data
offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While …