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 …

Challenges and advances in clinical applications of mesenchymal stromal cells

T Zhou, Z Yuan, J Weng, D Pei, X Du, C He… - Journal of hematology & …, 2021 - Springer
Mesenchymal stromal cells (MSCs), also known as mesenchymal stem cells, have been
intensely investigated for clinical applications within the last decades. However, the majority …

μMap photoproximity labeling enables small molecule binding site mapping

SW Huth, JV Oakley, CP Seath, JB Geri… - Journal of the …, 2023 - ACS Publications
The characterization of ligand binding modes is a crucial step in the drug discovery process
and is especially important in campaigns arising from phenotypic screening, where the …

Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications

L Malinovska, V Cappelletti, D Kohler, I Piazza… - Nature protocols, 2023 - nature.com
Proteins regulate biological processes by changing their structure or abundance to
accomplish a specific function. In response to a perturbation, protein structure may be …

Recent advances in identifying protein targets in drug discovery

J Ha, H Park, J Park, SB Park - Cell chemical biology, 2021 - cell.com
Phenotype-based screening has emerged as an alternative route for discovering new
chemical entities toward first-in-class therapeutics. However, clarifying their mode of action …

Recent advances in machine learning applications in metabolic engineering

P Patra, BR Disha, P Kundu, M Das, A Ghosh - Biotechnology Advances, 2023 - Elsevier
Metabolic engineering encompasses several widely-used strategies, which currently hold a
high seat in the field of biotechnology when its potential is manifesting through a plethora of …

Predicting drug–target binding affinity through molecule representation block based on multi-head attention and skip connection

L Zhang, CC Wang, X Chen - Briefings in Bioinformatics, 2022 - academic.oup.com
Exiting computational models for drug–target binding affinity prediction have much room for
improvement in prediction accuracy, robustness and generalization ability. Most deep …

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

Y Hsiao, H Zhang, GX Li, Y Deng, F Yu… - Journal of Proteome …, 2024 - ACS Publications
The FragPipe computational proteomics platform is gaining widespread popularity among
the proteomics research community because of its fast processing speed and user-friendly …

[HTML][HTML] Machine learning in clinical decision making

L Adlung, Y Cohen, U Mor, E Elinav - Med, 2021 - cell.com
Machine learning is increasingly integrated into clinical practice, with applications ranging
from pre-clinical data processing, bedside diagnosis assistance, patient stratification …