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 …

Deep learning-based method for predicting and classifying the binding affinity of protein-protein complexes

R Nikam, K Yugandhar, MM Gromiha - Biochimica et Biophysica Acta (BBA) …, 2023 - Elsevier
Protein-protein interactions (PPIs) play a critical role in various biological processes.
Accurately estimating the binding affinity of PPIs is essential for understanding the …

In Silico Protein Structure Analysis for SARS-CoV-2 Vaccines Using Deep Learning

Y Matsuzaka, R Yashiro - BioMedInformatics, 2023 - mdpi.com
Protein three-dimensional structural analysis using artificial intelligence is attracting
attention in various fields, such as the estimation of vaccine structure and stability. In …

DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein–protein complexes upon mutation

R Nikam, S Jemimah, MM Gromiha - Bioinformatics, 2024 - academic.oup.com
Motivation Protein–protein interactions underpin many cellular processes and their
disruption due to mutations can lead to diseases. With the evolution of protein structure …

[HTML][HTML] PMSFF: Improved Protein Binding Residues Prediction through Multi-Scale Sequence-Based Feature Fusion Strategy

Y Li, X Nan, S Zhang, Q Zhou, S Lu, Z Tian - Biomolecules, 2024 - mdpi.com
Proteins perform different biological functions through binding with various molecules which
are mediated by a few key residues and accurate prediction of such protein binding residues …

A Reversible Spherical Geometric Conversion of Protein Backbone Structure Coordinate Matrix to Three Independent Vectors of ρ, θ and φ

W Li - 2024 - preprints.org
Due to the vast conformational space proteins can adopt, accurate and efficient prediction of
protein structure remains still a challenging task, coupled with the intricacies of interatomic …

Predicting Protein-Ligand Binding Affinities: A Machine Learning Approach

PA Akhil, N Sooraj, R Ani - 2024 Second International …, 2024 - ieeexplore.ieee.org
Molecular docking plays a vital role in drug development and molecular modeling, with the
accuracy of docking heavily reliant on the scoring function's reliability. Scoring functions …

VIEPred: Predicting Viral Immune Evasion with Multimodal Representation Learning

B Liang, N Wang, H Huang, Y Hou… - Journal of Physics …, 2024 - iopscience.iop.org
Predicting coronaviral immune evasion is crucial for identifying and responding to new
COVID-19 variants in advance, thereby optimizing vaccine development and public health …

Prediction of binding sites of GPCRs based on 3D convolutional neural networks

JF Yu, Y Zhang, J Lv - bioRxiv, 2024 - biorxiv.org
G protein-coupled receptors are a class of receptor proteins located on the cell membrane,
regulating the perception and response of cells to various external signals. Identifying the …