Machine Learning for Sequence and Structure-Based Protein–Ligand Interaction Prediction

Y Zhang, S Li, K Meng, S Sun - Journal of Chemical Information …, 2024 - ACS Publications
Developing new drugs is too expensive and time-consuming. Accurately predicting the
interaction between drugs and targets will likely change how the drug is discovered …

Computational chemistry in structure-based solute carrier transporter drug design: Recent advances and future perspectives

G Tu, T Fu, G Zheng, B Xu, R Gou, D Luo… - Journal of chemical …, 2024 - ACS Publications
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are
involved in the transportation of diverse solute ions and small molecules into cells. There are …

Defining the cell surface cysteinome using two-step enrichment proteomics

T Yan, LM Boatner, L Cui, PJ Tontonoz, KM Backus - JACS Au, 2023 - ACS Publications
The plasma membrane proteome is a rich resource of functionally important and
therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy …

Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort

AM Illig, NE Siedhoff, MD Davari… - Journal of Chemical …, 2024 - ACS Publications
Protein engineering through directed evolution and (semi) rational approaches is routinely
applied to optimize protein properties for a broad range of applications in industry and …

Quantifying the hardness of bioactivity prediction tasks for transfer learning

H Fooladi, S Hirte, J Kirchmair - Journal of Chemical Information …, 2024 - ACS Publications
Today, machine learning methods are widely employed in drug discovery. However, the
chronic lack of data continues to hamper their further development, validation, and …

Non-alcoholic fatty liver disease promotes breast cancer progression through upregulated hepatic fibroblast growth factor 21

Y Sui, Q Liu, C Xu, K Ganesan, Z Ye, Y Li, J Wu… - Cell Death & …, 2024 - nature.com
Non-alcoholic fatty liver disease (NAFLD) has been shown to influence breast cancer
progression, but the underlying mechanisms remain unclear. In this study, we investigated …

Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks

K Castillo-Mendieta, G Agüero-Chapin… - npj Systems Biology …, 2024 - nature.com
Peptides are promising drug development frameworks that have been hindered by intrinsic
undesired properties including hemolytic activity. We aim to get a better insight into the …

Structure-Guided Chemical Optimization of Bicyclic Peptide (Bicycle) Inhibitors of Angiotensin-Converting Enzyme 2

MAJ Harman, SJ Stanway, H Scott… - Journal of Medicinal …, 2023 - ACS Publications
Angiotensin-converting enzyme 2 (ACE2) is a metalloprotease that cleaves angiotensin II, a
peptide substrate involved in the regulation of hypertension. Here, we identified a series of …

Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference

H Peng, H Wang, W Kong, J Li, WWB Goh - Nature Communications, 2024 - nature.com
Identification of differentially expressed proteins in a proteomics workflow typically
encompasses five key steps: raw data quantification, expression matrix construction, matrix …

A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening

E Elisée, L Ducrot, R Méheust, K Bastard… - Nature …, 2024 - nature.com
Native amine dehydrogenases offer sustainable access to chiral amines, so the search for
scaffolds capable of converting more diverse carbonyl compounds is required to reach the …