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

24,037 views
35 citations

Original Research

Published on 16 Sep 2024

Graph neural pre-training based drug-target affinity prediction

in Computational Genomics

Qing Ye
Yaxin Sun

Frontiers in Genetics

doi 10.3389/fgene.2024.1452339

3,360 views
4 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

5,815 views
6 citations

Original Research

Published on 20 Mar 2025

MDNN-DTA: a multimodal deep neural network for drug-target affinity prediction

in Computational Genomics

Xu Gao
Mengfan Yan
Chengwei Zhang
Gang Wu
Jiandong Shang
Congxiang Zhang
Kecheng Yang

Frontiers in Genetics

doi 10.3389/fgene.2025.1527300

2,789 views
2 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

7,975 views
56 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

3,732 views
3 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

34,649 views
122 citations

Original Research

Published on 30 May 2022

Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations

in B Cell Biology

Mabel T. Y. Wong
Sebastian Kelm
Xiaofeng Liu
Richard D. Taylor
Terry Baker
Jonathan W. Essex

Frontiers in Immunology

doi 10.3389/fimmu.2022.884110

4,612 views
5 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

1,152 views

Methods

Published on 09 Feb 2017

Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity

in B Cell Biology

Simon Marillet
Marie-Paule Lefranc
Pierre Boudinot
Frédéric Cazals

Frontiers in Immunology

doi 10.3389/fimmu.2017.00034

6,000 views
26 citations

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

11,882 views
75 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

10,745 views
21 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

3,169 views

Original Research

Published on 02 Jul 2021

Expression Profiling and Functional Analysis of Candidate Col10a1 Regulators Identified by the TRAP Program

in Genetics of Common and Rare Diseases

Huiqin Bian
Ting Zhu
Yuting Liang
Ruoxuan Hei
Xiaojing Zhang
Xiaochen Li
Jinnan Chen
Yaojuan Lu
Junxia Gu
Longwei Qiao

Frontiers in Genetics

doi 10.3389/fgene.2021.683939

6,482 views
14 citations

Articles

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

Graph neural pre-training based drug-target affinity prediction

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

MDNN-DTA: a multimodal deep neural network for drug-target affinity prediction

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

Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations

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

Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity

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

Expression Profiling and Functional Analysis of Candidate Col10a1 Regulators Identified by the TRAP Program