Paper and Preprints

Papers

@ gRED

15. Grambow, C. A.; ‡  Weir, H.; Diamant, N. L.; Tseng, A. M.; Biancalani, T.; Scalia, G.; Chuang, K. V. ‡  “RINGER: Rapid Conformer Generation for Macrocycles with Sequence-Conditioned Internal Coordinate Diffusion.” 2023, arXiv: 2305.19800 [q-bio.BM] https://arxiv.org/abs/2305.19800.

14. Grambow, C. A.;‡ Weir, H.; Cunningham, C. N.; Biancalani, T.; Chuang, K. V.‡ “CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning.” 2023, arXiv: 2305.08057 [q-bio.BM]. https://arxiv.org/abs/2305.08057. CREMP available for download on Zenodo.

13. Diamant, N. L.; Tseng, A. M.; Chuang, K. V.; Biancalani, T.; Scalia, G. “Improving Graph Generation by Restricting Graph Bandwidth.” Accepted at ICML 2023. arXiv:2301.10857 [cs.LG]. https://arxiv.org/abs/2301.10857 .

12. Astango, A.; Diamant, N. L.; Lu, Z.; Biancalani, T.; Scalia, G.;‡ Chuang, K. V.‡ “A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning.” NeurIPS AI4Science 2022.

@ UCSF

11. Chuang, K. V.; Keiser, M. J. “Attention-Based Learning on Molecular Ensembles.” Machine Learning for Molecules Workshop at NeurIPS 2020.

10. Chuang, K. V.; Gunsalus, L. M.; Keiser, M. J. “Learning Molecular Representations for Medicinal Chemistry.” J. Med. Chem. 2020, 63, 16, 8705. DOI: 10.1021/acs.jmedchem.0c00385.

9. Tang, Z.; Chuang, K.V.; DeCarli, C., Jin, L.-W.; Beckett, L.; Keiser, M.J.‡, Dugger, B. D.‡ “Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline.” Nat. Commun. 2019, 10, 2173.

8.   Chuang, K. V.; Keiser, M. J. “Comment on ‘Predicting reaction performance in C-N cross-coupling using machine learning.’” Science, 2018, 362, 6416. DOI: 10.1126/science.aat8603.

7.   Chuang, K. V.; Keiser, M. J. “Adversarial Controls for Scientific Machine Learning.” ACS Chem. Bio. 2018, 13, 2819.

@ Caltech

6.   Chuang, K. V.; Kieffer, M. E.; Reisman, S. E. “A Mild and General Larock Indolization Protocol for the Preparation of Unnatural Tryptophans.” Org. Lett. 2016, 18, 4750.

5.   Chuang, K. V.*; Xu, C.*; Reisman, S. E.; “A 15-Step Synthesis of (+)-Ryanodol.” Science. 2016, 353, 912.

 4.   Kieffer, M. E.*; Chuang, K. V.*; Reisman, S. E. “Copper-Catalyzed Diastereoselective Arylation of Tryptophan Derivatives: Total Synthesis of (+)-Naseseazines A and B.” J. Am. Chem. Soc. 2013, 135, 5557-5560.

3.  Kieffer, M. E.; Chuang, K. V.; Reisman, S. E. “A Copper-Catalyzed Arylation of Tryptamines for the Direct Synthesis of Aryl Pyrroloindolines.” Chem. Sci. 2012, 3, 3170-3174.

2. Chuang, K. V.; Navarro, R.; Reisman, S. E. “Short, Enantioselective Total Syntheses of (–)-8 Demethoxyrunanine and (–)-Cepharatines A, C, and D.” Angew. Chem. Int. Ed. 2011, 50, 9447-9451.

1. Chuang, K. V.; Navarro, R.; Reisman, S. E. “Benzoquinone-Derived Sulfinyl Imines as Versatile Intermediates for Alkaloid Synthesis: Total Synthesis of (–)-3-Demethoxyerythratidinone.” Chem. Sci. 2011, 2, 1086-1089.

Patent

1. Reisman, S. E.; Chuang, K. V.; Xu, C. “Synthetic route to anhydroryanodol, ryanodol and structural analogues.” US Patent #9,862,696.