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Updated: Mar 29, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
AI-MedCraft: A Strategy-Driven AI Platform for Multi-Objective Molecular Design
Khaled Barakat1, Michael Jordy Rojas Ruiz1, Hazem Ahmed1
1Thoth Biosimulations Inc., 4560 Enterprise Square, 10230 Jasper Avenue, Edmonton, Alberta T5J 4P6, Canada.
Abstract:
Small-molecule drug discovery requires balancing potency, selectivity, solubility, safety, and synthetic feasibility, among other interdependent properties. Yet most computational workflows address these properties sequentially or collapse them into fixed weighted scores. Although artificial intelligence has accelerated molecular design, many platforms struggle to handle explicit multiobjective trade-offs. Here, we present AI-MedCraft, a strategy-driven molecular design framework that applies adaptive, Pareto-guided reinforcement learning to optimize multiple objectives concurrently within a unified workflow. When structural information is available, physics-aware scoring is incorporated to support binding-competent designs. In a structure-based benchmark on the solubility rescue of the BTK inhibitor GDC-0834, AI-MedCraft achieves broader Pareto-front coverage than the scalar-reward reinforcement learning framework REINVENT 4 under matched objectives and computational cost. In a second case study, AI-MedCraft redesigns Efavirenz to retain HIV-1 reverse transcriptase engagement while reducing predicted 5-HT2A off-target binding, demonstrating its use in multiconstraint molecular optimization.
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