[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

Open-source machine learning in computational chemistry

A Hagg, KN Kirschner - Journal of Chemical Information and …, 2023 - ACS Publications
The field of computational chemistry has seen a significant increase in the integration of
machine learning concepts and algorithms. In this Perspective, we surveyed 179 open …

Protein–protein contact prediction by geometric triangle-aware protein language models

P Lin, H Tao, H Li, SY Huang - Nature Machine Intelligence, 2023 - nature.com
Abstract Information regarding the residue–residue distance between interacting proteins is
important for modelling the structures of protein complexes, as well as being valuable for …

Machine learning on protein–protein interaction prediction: models, challenges and trends

T Tang, X Zhang, Y Liu, H Peng, B Zheng… - Briefings in …, 2023 - academic.oup.com
Protein–protein interactions (PPIs) carry out the cellular processes of all living organisms.
Experimental methods for PPI detection suffer from high cost and false-positive rate, hence …

Unifying structural descriptors for biological and bioinspired nanoscale complexes

M Cha, EST Emre, X Xiao, JY Kim, P Bogdan… - Nature Computational …, 2022 - nature.com
Biomimetic nanoparticles are known to serve as nanoscale adjuvants, enzyme mimics and
amyloid fibrillation inhibitors. Their further development requires better understanding of …

HNSPPI: a hybrid computational model combing network and sequence information for predicting protein–protein interaction

S Xie, X Xie, X Zhao, F Liu, Y Wang… - Briefings in …, 2023 - academic.oup.com
Most life activities in organisms are regulated through protein complexes, which are mainly
controlled via Protein–Protein Interactions (PPIs). Discovering new interactions between …

Recent advances in deep learning for protein-protein interaction analysis: A comprehensive review

M Lee - Molecules, 2023 - mdpi.com
Deep learning, a potent branch of artificial intelligence, is steadily leaving its transformative
imprint across multiple disciplines. Within computational biology, it is expediting progress in …

Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges

X Qi, Y Zhao, Z Qi, S Hou, J Chen - Molecules, 2024 - mdpi.com
Drug discovery plays a critical role in advancing human health by developing new
medications and treatments to combat diseases. How to accelerate the pace and reduce the …

The power of computational proteomics platforms to decipher protein-protein interactions

M González-Avendaño, J López… - Current Opinion in …, 2024 - Elsevier
Adopting computational tools for analyzing extensive biological datasets has profoundly
transformed our understanding and interpretation of biological phenomena. Innovative …

[HTML][HTML] SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer

W Hu, M Ohue - Computational and Structural Biotechnology Journal, 2024 - Elsevier
Rapid advancements in protein sequencing technology have resulted in gaps between
proteins with identified sequences and those with mapped structures. Although sequence …