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2025
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| Online Access: | https://doi.org/10.5281/zenodo.18067231 |
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| _version_ | 1866901407123111936 |
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| author | KUMAR, PRABIN |
| author_facet | KUMAR, PRABIN |
| contents | <div> <div> <div> <div> <div dir="auto"> <div> <div> <h3><strong>Description</strong></h3> <p>Adaptive Protein Design and Optimization (APDO) is a lightweight, modular research framework that demonstrates how protein-like three-dimensional structures can emerge purely through adaptive energy minimization.</p> <p>Unlike traditional protein folding pipelines that rely on computationally expensive molecular dynamics or physics-heavy force fields, APDO operates on a simplified energy landscape and iterative optimization loop. Despite its abstraction, the framework consistently converges toward lower-energy, structured conformations from random initial states.</p> <p>This project provides a proof-of-concept that protein structure optimization is fundamentally governed by energy landscapes rather than simulation fidelity. APDO is designed for research, education, and experimentation in protein design, molecular optimization, and AI-driven scientific discovery.</p> <h3><strong>Key Contributions</strong></h3> <ul> <li> <p>Demonstrates energy-driven emergence of protein-like structures</p> </li> <li> <p>Fully modular architecture (energy, optimization, core logic)</p> </li> <li> <p>Lightweight and reproducible on standard CPU environments</p> </li> <li> <p>Extendable to ML-based energy models and hybrid pipelines</p> </li> </ul> <h3><strong>Applications</strong></h3> <p>Protein design • Molecular optimization • Computational biology education • AI-assisted scientific modeling</p> <h3><strong>Keywords</strong></h3> <p>Protein Design, Energy Minimization, Computational Biology, Optimization Algorithms, AI for Science, Protein Folding, Structural Biology</p> <h3><strong>License</strong></h3> <p>MIT License</p> </div> </div> </div> </div> </div> </div> <div> <div> <div> </div> <div> <div> </div> </div> </div> </div> </div> <div>https://github.com/pksms078-ai/Adaptive-Protein-Design-and-Optimization-APDO-/releases/tag/APDO1</div> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18067231 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Adaptive Protein Design and Optimization (APDO): An Energy-Driven Framework for Protein Structure Optimization KUMAR, PRABIN <div> <div> <div> <div> <div dir="auto"> <div> <div> <h3><strong>Description</strong></h3> <p>Adaptive Protein Design and Optimization (APDO) is a lightweight, modular research framework that demonstrates how protein-like three-dimensional structures can emerge purely through adaptive energy minimization.</p> <p>Unlike traditional protein folding pipelines that rely on computationally expensive molecular dynamics or physics-heavy force fields, APDO operates on a simplified energy landscape and iterative optimization loop. Despite its abstraction, the framework consistently converges toward lower-energy, structured conformations from random initial states.</p> <p>This project provides a proof-of-concept that protein structure optimization is fundamentally governed by energy landscapes rather than simulation fidelity. APDO is designed for research, education, and experimentation in protein design, molecular optimization, and AI-driven scientific discovery.</p> <h3><strong>Key Contributions</strong></h3> <ul> <li> <p>Demonstrates energy-driven emergence of protein-like structures</p> </li> <li> <p>Fully modular architecture (energy, optimization, core logic)</p> </li> <li> <p>Lightweight and reproducible on standard CPU environments</p> </li> <li> <p>Extendable to ML-based energy models and hybrid pipelines</p> </li> </ul> <h3><strong>Applications</strong></h3> <p>Protein design • Molecular optimization • Computational biology education • AI-assisted scientific modeling</p> <h3><strong>Keywords</strong></h3> <p>Protein Design, Energy Minimization, Computational Biology, Optimization Algorithms, AI for Science, Protein Folding, Structural Biology</p> <h3><strong>License</strong></h3> <p>MIT License</p> </div> </div> </div> </div> </div> </div> <div> <div> <div> </div> <div> <div> </div> </div> </div> </div> </div> <div>https://github.com/pksms078-ai/Adaptive-Protein-Design-and-Optimization-APDO-/releases/tag/APDO1</div> |
| title | Adaptive Protein Design and Optimization (APDO): An Energy-Driven Framework for Protein Structure Optimization |
| url | https://doi.org/10.5281/zenodo.18067231 |