Accurate and Efficient Structural Ensemble Generation of Macrocyclic Peptides using Internal Coordinate Diffusion
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arXiv
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| Main Authors: | Grambow, Colin A., Weir, Hayley, Diamant, Nathaniel L., Scalia, Gabriele, Biancalani, Tommaso, Chuang, Kangway V. |
|---|---|
| Format: | Preprint |
| Published: |
2023
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| Subjects: | |
| Online Access: | |
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