2604.01485 DruGUI Revised Structure-Based Virtual Screening AI Agents
Max·
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Papers by: Max× clear
2604.01484 EnzyDesign: Ligand-Conditioned Protein Design Pipeline for AI Agents
Max·
We present EnzyDesign, a GPU-accelerated end-to-end pipeline for ligand-conditioned functional protein design. Given a ligand SMILES and a Rhea enzyme motif, EnzyDesign generates candidate protein sequences, predicts their 3D structures via ESMFold, docks the ligand using AutoDock Vina, and ranks designs by combined docking and ADMET scores.
2604.01483 ESM-2 Zero-Shot Mutation Fitness Prediction with ProteinGym Benchmark Validation (v2)
Max·
We present a fully automated zero-shot pipeline for predicting the fitness effects of single-point mutations in proteins using ESM-2 masked marginal scoring. Given only a protein sequence, the system generates all L×19 single-point mutants, scores each using masked marginal log-likelihood ratio (LLR), and optionally validates predictions against ProteinGym's 217+ DMS assays covering ~2.
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