Artificial intelligence-driven drug development against autoimmune diseases

P Moingeon - Trends in pharmacological sciences, 2023 - cell.com
Artificial intelligence (AI)-based predictive models are being used to foster a precision
medicine approach to treat complex chronic diseases such as autoimmune and …

Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics

J Lai, H Huang, M Lin, Y Xu, X Li, B Sun - Frontiers in Microbiology, 2023 - frontiersin.org
Petro-plastic wastes cause serious environmental contamination that require effective
solutions. Developing alternatives to petro-plastics and exploring feasible degrading …

Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

HK Neikes, KW Kliza, C Gräwe, RA Wester… - Nature …, 2023 - nature.com
Transcription factor binding across the genome is regulated by DNA sequence and
chromatin features. However, it is not yet possible to quantify the impact of chromatin context …

Data‐Driven Protein Engineering for Improving Catalytic Activity and Selectivity

YF Ao, M Dörr, MJ Menke, S Born, E Heuson… - …, 2024 - Wiley Online Library
Protein engineering is essential for altering the substrate scope, catalytic activity and
selectivity of enzymes for applications in biocatalysis. However, traditional approaches, such …

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

J Wu, J Lv, L Zhao, R Zhao, T Gao, Q Xu, D Liu… - Science of the Total …, 2023 - Elsevier
Molecular simulation has been widely used to study microbial proteins' structural
composition and dynamic properties, such as volatility, flexibility, and stability at the …

High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

A Li, R Voleti, M Lee, D Gagoski, NH Shah - Elife, 2023 - elifesciences.org
Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have binding specificities
that depend on the amino acid sequence surrounding the target (phospho) tyrosine residue …

HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra‐large …

KI Popov, J Wellnitz, T Maxfield… - Molecular …, 2024 - Wiley Online Library
Recent rapid expansion of make‐on‐demand, purchasable, chemical libraries comprising
dozens of billions or even trillions of molecules has challenged the efficient application of …

Disentangling representations in restricted boltzmann machines without adversaries

J Fernandez-de-Cossio-Diaz, S Cocco, R Monasson - Physical Review X, 2023 - APS
A goal of unsupervised machine learning is to build representations of complex high-
dimensional data, with simple relations to their properties. Such disentangled …

TransVAE-DTA: Transformer and variational autoencoder network for drug-target binding affinity prediction

C Zhou, Z Li, J Song, W Xiang - Computer Methods and Programs in …, 2024 - Elsevier
Background and objective Recent studies have emphasized the significance of
computational in silico drug-target binding affinity (DTA) prediction in the field of drug …

A systematic survey in geometric deep learning for structure-based drug design

Z Zhang, J Yan, Q Liu, E Chen, M Zitnik - arXiv preprint arXiv:2306.11768, 2023 - arxiv.org
Structure-based drug design (SBDD) utilizes the three-dimensional geometry of proteins to
identify potential drug candidates. Traditional methods, grounded in physicochemical …