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Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
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AI
DOI：10.1021/acs.jcim.2c00695.png)
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摘要
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Machine learning-based drug discovery success depends on molecular representation. Yet traditional molecular fingerprints omit both the protein and pointers back to structural information that would enable better model interpretability. Therefore, we propose LUNA, a Python 3 toolkit that calculates and encodes protein-ligand interactions into new hashed fingerprints inspired by Extended Connectivity FingerPrint (ECFP): EIFP (Extended Interaction FingerPrint), FIFP (Functional Interaction FingerPrint), and Hybrid Interaction FingerPrint (HIFP). LUNA also provides visual strategies to make the fingerprints interpretable. We performed three major experiments exploring the fingerprints' use. First, we trained machine learning models to reproduce DOCK3.7 scores using 1 million docked Dopamine D4 complexes. We found that EIFP-4,096 performed (R-2 = 0.61) superior to related molecular and interaction fingerprints. Second, we used LUNA to support interpretable machine learning models. Finally, we demonstrate that interaction fingerprints can accurately identify similarities across molecular complexes that other fingerprints overlook. Hence, we envision LUNA and its interface fingerprints as promising methods for machine learning-based virtual screening campaigns. LUNA is freely available at https://github.com/keiserlab/LUNA.
Keyword:
BINDING-SITE
ATOM PAIRS
WEB SERVER
LIGAND
DESCRIPTORS
INHIBITORS
2D
IDENTIFICATION
REPRESENTATION
CHEMISTRY
期刊
IF:
5.3
论文数:
9.1K
被引数:
4.0W
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引用论文
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KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural NetworksKDEEP: 通过3d卷积神经网络预测蛋白质-配体绝对结合亲和力
PREAI
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