Psc-cpi: Multi-scale protein sequence-structure contrasting for efficient and generalizable compound-protein interaction prediction

L Wu, Y Huang, C Tan, Z Gao, B Hu, H Lin… - Proceedings of the …, 2024‏ - ojs.aaai.org
Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of
compound-protein interactions for rational drug discovery. Existing deep learning-based …

Current computational tools for protein lysine acylation site prediction

Z Qin, H Ren, P Zhao, K Wang, H Liu… - Briefings in …, 2024‏ - academic.oup.com
As a main subtype of post-translational modification (PTM), protein lysine acylations (PLAs)
play crucial roles in regulating diverse functions of proteins. With recent advancements in …

[HTML][HTML] Applications of artificial intelligence to lipid nanoparticle delivery

Y Yuan, Y Wu, J Cheng, K Yang, Y **a, H Wu, X Pan - Particuology, 2024‏ - Elsevier
Lipid nanoparticles (LNPs) are nanocarriers composed of four lipid components and can be
used for gene therapy, protein replacement, and vaccine development. However, LNPs also …

Ppflow: Target-aware peptide design with torsional flow matching

H Lin, O Zhang, H Zhao, D Jiang, L Wu, Z Liu, Y Huang… - bioRxiv, 2024‏ - biorxiv.org
Therapeutic peptides have proven to have great pharmaceutical value and potential in
recent decades. However, methods of AI-assisted peptide drug discovery are not fully …

Interpretable machine learning of amino acid patterns in proteins: a statistical ensemble approach

A Braghetto, E Orlandini, M Baiesi - Journal of Chemical Theory …, 2023‏ - ACS Publications
Explainable and interpretable unsupervised machine learning helps one to understand the
underlying structure of data. We introduce an ensemble analysis of machine learning …

Recent advances in interpretable machine learning using structure-based protein representations

LF Vecchietti, M Lee, B Hangeldiyev, H Jung… - arxiv preprint arxiv …, 2024‏ - arxiv.org
Recent advancements in machine learning (ML) are transforming the field of structural
biology. For example, AlphaFold, a groundbreaking neural network for protein structure …

MProt-DPO: Breaking the ExaFLOPS Barrier for Multimodal Protein Design Workflows with Direct Preference Optimization

G Dharuman, K Hippe, A Brace… - … Conference for High …, 2024‏ - ieeexplore.ieee.org
We present a scalable, end-to-end workflow for protein design. By augmenting protein
sequences with natural language descriptions of their biochemical properties, we train …

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 …