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Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
Published on: September 26, 2025
Model Gateway: Management platform for model-driven drug discovery
Yan-Shiun Wu1, Sai Mahit Vaddadi2, Zachary A Rollins2
1Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA; Convergent Bioscience and Technology Institute, Indiana University, Indianapolis, IN 46202, USA; Department of Biomedical Engineering and Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University, Indianapolis, IN 46202, USA.
Abstract:
Pharmaceutical drug discovery demands machine learning (ML) infrastructure that goes beyond general-purpose Machine Learning Operations: inference-time composition of multiple models for multiparameter optimization, version management for physics-based models without serialized ML artifacts, enterprise compound library precomputation and governance structured around scientific organizational units rather than generic access controls. No existing commercial or open-source platform simultaneously addresses this full set of requirements. This review presents the Model Gateway, a cloud-based platform for managing ML and scientific computational models across drug discovery pipelines, providing centralized version control, pharma-structured governance, asynchronous execution, consensus model orchestration, automated retraining and a unified application programming interface service for heterogeneous clients, including molecular design suites and large language model agents. In production at Eli Lilly, the platform governs more than 200 deployed models spanning small-molecule, peptide and antibody modalities and serves more than five downstream applications across all phases of the Design-Make-Test-Analyze cycle.
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