Physicochemical rule-embedded generative modeling for constrained peptide therapeutics
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Updated: Oct 31, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Yuzhou Wang1, Dongsheng Cao2, Xiangzheng Fu3
1College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Abstract:
Constrained peptides couple covalent topology, stereochemistry, three-dimensional structure, conformational dynamics and developability. We review physicochemical rule embedding across chemical-language, target-conditioned structural, geometric, atom-bond, ensemble and property-guided generative models, distinguishing generated molecular objects from downstream inference and predictions from prospective evidence. We identify limitations in chemical coverage, applicability, uncertainty and pipeline attribution, and routes towards identity-preserving, environment-aware and experimentally calibrated design.
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