Binding Affinity Prediction | List of Frontiers open access articles

Perspective

Published on 16 Dec 2022

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

in Drug Discovery in Bioinformatics

Zhongliang Guo
Rui Yamaguchi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1065703

24,973 views
39 citations

Original Research

Published on 03 Jan 2025

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

in Experimental Pharmacology and Drug Discovery

Hyojin Kim
Heesung Shim
Aditya Ranganath
Stewart He
Garrett Stevenson
Jonathan E. Allen

Frontiers in Pharmacology

doi 10.3389/fphar.2024.1518875

6,746 views
6 citations

Original Research

Published on 19 Feb 2021

SE-OnionNet: A Convolution Neural Network for Protein–Ligand Binding Affinity Prediction

in Computational Genomics

Shudong Wang
Dayan Liu
Mao Ding
Zhenzhen Du
Yue Zhong
Tao Song
Jinfu Zhu
Renteng Zhao

Frontiers in Genetics

doi 10.3389/fgene.2020.607824

8,392 views
57 citations

Original Research

Published on 10 Jul 2024

GIHP: Graph convolutional neural network based interpretable pan-specific HLA-peptide binding affinity prediction

in Computational Genomics

Lingtao Su
Yan Yan
Bo Ma
Shiwei Zhao
Zhenyu Cui

Frontiers in Genetics

doi 10.3389/fgene.2024.1405032

4,068 views
5 citations

Review

Published on 17 Jun 2022

Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

in Drug Discovery in Bioinformatics

Rocco Meli
Garrett M. Morris
Philip C. Biggin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.885983

36,592 views
134 citations

Review

Published on 12 Jan 2026

Recent trends in machine learning and deep learning-based prediction of G-protein coupled receptor-ligand binding affinities

in Drug Discovery in Bioinformatics

Joshua Stephenson
Konda Reddy Karnati

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1712577

1,972 views

Original Research

Published on 06 Jul 2022

ATM-TCR: TCR-Epitope Binding Affinity Prediction Using a Multi-Head Self-Attention Model

in T Cell Biology

Michael Cai
Seojin Bang
Pengfei Zhang
Heewook Lee

Frontiers in Immunology

doi 10.3389/fimmu.2022.893247

12,562 views
83 citations

Original Research

Published on 30 Jun 2022

3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors

in Clinical and Diagnostic Microbiology and Immunology

Vikas Kumar
Shraddha Parate
Danishuddin
Amir Zeb
Pooja Singh
Gihwan Lee
Tae Sung Jung
Keun Woo Lee
Min Woo Ha

Frontiers in Cellular and Infection Microbiology

doi 10.3389/fcimb.2022.909111

11,352 views
24 citations

Methods

Published on 28 Oct 2022

DPB-NBFnet: Using neural Bellman-Ford networks to predict DNA-protein binding

in Experimental Pharmacology and Drug Discovery

Jing Li
Linlin Zhuo
Xinze Lian
Shiyao Pan
Lei Xu

Frontiers in Pharmacology

doi 10.3389/fphar.2022.1018294

3,544 views
1 citation

Articles

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

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

SE-OnionNet: A Convolution Neural Network for Protein–Ligand Binding Affinity Prediction

GIHP: Graph convolutional neural network based interpretable pan-specific HLA-peptide binding affinity prediction

Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

Recent trends in machine learning and deep learning-based prediction of G-protein coupled receptor-ligand binding affinities

ATM-TCR: TCR-Epitope Binding Affinity Prediction Using a Multi-Head Self-Attention Model

3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors

DPB-NBFnet: Using neural Bellman-Ford networks to predict DNA-protein binding