Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

K Gao, R Wang, J Chen, L Cheng, J Frishcosy… - Chemical …, 2022 - ACS Publications
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …

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 …

Persistent Laplacian projected Omicron BA. 4 and BA. 5 to become new dominating variants

J Chen, Y Qiu, R Wang, GW Wei - Computers in Biology and Medicine, 2022 - Elsevier
Due to its high transmissibility, Omicron BA. 1 ousted the Delta variant to become a
dominating variant in late 2021 and was replaced by more transmissible Omicron BA. 2 in …

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function

Z Wang, L Zheng, S Wang, M Lin, Z Wang… - Briefings in …, 2023 - academic.oup.com
The recently reported machine learning-or deep learning-based scoring functions (SFs)
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …

Emerging dominant SARS-CoV-2 variants

J Chen, R Wang, Y Hozumi, G Liu, Y Qiu… - Journal of chemical …, 2022 - ACS Publications
Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get …

Persistent Dirac for molecular representation

JJ Wee, G Bianconi, K Xia - Scientific Reports, 2023 - nature.com
Molecular representations are of fundamental importance for the modeling and analysing
molecular systems. The successes in drug design and materials discovery have been …

Persistent hyperdigraph homology and persistent hyperdigraph Laplacians

D Chen, J Liu, J Wu, GW Wei - arXiv preprint arXiv:2304.00345, 2023 - arxiv.org
Hypergraphs are useful mathematical models for describing complex relationships among
members of a structured graph, while hyperdigraphs serve as a generalization that can …

Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

Machine learning methods for protein-protein binding affinity prediction in protein design

Z Guo, R Yamaguchi - Frontiers in Bioinformatics, 2022 - frontiersin.org
Protein-protein interactions govern a wide range of biological activity. A proper estimation of
the protein-protein binding affinity is vital to design proteins with high specificity and binding …

Fingerprint-enhanced graph attention network (FinGAT) model for antibiotic discovery

HY Choo, JJ Wee, C Shen, K Xia - Journal of Chemical …, 2023 - ACS Publications
Artificial Intelligence (AI) techniques are of great potential to fundamentally change antibiotic
discovery industries. Efficient and effective molecular featurization is key to all highly …