DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
Open accessAbstract
Comprehensive characterization of ligand-binding sites is invaluable to infer molecular functions of hypothetical proteins, trace evolutionary relationships between proteins, engineer enzymes to achieve a desired substrate specificity, and develop drugs with improved selectivity profiles. These research efforts pose significant challenges owing to the fact that similar pockets are commonly observed across different folds, leading to the high degree of promiscuity of ligand-protein interactions at the system-level. On that account, novel algorithms to accurately classify binding sites are needed. Deep learning is attracting a significant attention due to its successful applications in a wide range of disciplines. In this communication, we present DeepDrug3D, a new approach to characterize and classify binding pockets in proteins with deep learning. It employs a state-of-the-art convolutional neural network in which biomolecular structures are represented as voxels assigned interaction energy-based attributes. The current implementation of DeepDrug3D, trained to detect and classify nucleotide- and heme-binding sites, not only achieves a high accuracy of 95%, but also has the ability to generalize to unseen data as demonstrated for steroid-binding proteins and peptidase enzymes. Interestingly, the analysis of strongly discriminative regions of binding pockets reveals that this high classification accuracy arises from learning the patterns of specific molecular interactions, such as hydrogen bonds, aromatic and hydrophobic contacts. DeepDrug3D is available as an open-source program at https://github.com/pulimeng/DeepDrug3D with the accompanying TOUGH-C1 benchmarking dataset accessible from https://osf.io/enz69/.
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AI/ML models have been applied to identification of potential pockets, especially up-ranking of the most ligandable ones.
“AI/ML models have been applied to the identification of these potential pockets, and especially to the up-ranking of the most ligandable ones.138”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [138]
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- Authors
- Pu, L., Govindaraj, R. G., Lemoine, J. M., Wu, H.-C., & Brylinski, M.
- Affiliations
- Louisiana State University (US)
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-02-04
- Volume
- 15
- Issue
- 2
- Pages
- e1006718
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC6375647
- OpenAlex
- W2914877211
- Cited by
- 133
- References
- 96
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 23 · 2023: 14 · 2022: 28 · 2021: 21 · 2020: 21 · 2019: 8
- FWCI
- 13.24
- Type
- journal article
- Language
- en
- Update notices
- new_version (2019-02-14)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Civil War Book Review (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of General Medical Sciences (R35GM119524)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- convolutional neural networks, nucleotide binding site, heme binding site, steroid binding proteins, protein structure
- MeSH terms
- Deep Learning, Algorithms, Binding Sites, Ligands, Models, Molecular, Protein Binding, Proteins, Neural Networks, Computer, Computational Biology, Databases, Protein
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