Structure-based, deep-learning models for protein-ligand binding affinity prediction

Debby D. Wang, Wenhui Wu, Ran Wang

Journal of Cheminformatics 2024 article cited by 49

importance 7/10 ai assisted Computational Drug Discovery Methods drug discovery stage: research

Predicting protein-ligand binding affinity from structure is a key open problem in computational drug discovery needing better methods.

Accurate binding affinity prediction could speed up drug discovery and reduce its cost.

A review of structure-based deep-learning approaches for binding affinity prediction, with a model taxonomy and uniform re-evaluation of representative models.

not stated in source

Review organizes and compares existing models; benefit to drug discovery is described as potential, not demonstrated.

Venue Journal of Cheminformatics
Published 2024
Work type article
Authors Debby D. Wang, Wenhui Wu, Ran Wang
Citations 49 (OpenAlex, at import time)
References 69
Model or method not stated in source
Organization not stated in source
Primary source https://doi.org/10.1186/s13321-023-00795-9
Open access gold
Keywords deep learning, protein-ligand, binding affinity, drug discovery, review
7 / 10

significant — thousands to millions affected

Binding affinity prediction is a key open problem in drug discovery, a foundational field; benefit described as potential, no scale stated.

Basis: inferred. Judged from the source text, which gives no explicit scale. Stated scale: not stated in source. Method and limits.

# Paper Year Citations Importance
1 AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
Mihály Váradi, Stephen Anyango, Mandar Deshpande, Sreenath Sasidharan...
2021 7,782
9
2 Evolutionary-scale prediction of atomic-level protein structure with a language model
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting L...
2023 5,455
9
3 Accurate prediction of protein structures and interactions using a three-track neural network
Minkyung Baek, Frank DiMaio, Ivan V. Anishchenko, Justas Dauparas, Ser...
2021 5,468
9
4 De novo design of protein structure and function with RFdiffusion
Joseph L. Watson, David Juergens, Nathaniel R. Bennett, Brian L. Tripp...
2023 2,294
9
5 Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins
Rebecca Buller, Jiřı́ Damborský, Donald Hilvert, Uwe T. Bornscheuer
2024 40
9