Ruffolo JA - Search Results

1

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies.

Ruffolo JA, Chu LS, Mahajan SP, Gray JJ. Ruffolo JA, et al. Nat Commun. 2023 Apr 25;14(1):2389. doi: 10.1038/s41467-023-38063-x. Nat Commun. 2023. PMID: 37185622 Free PMC article.

2

Modeling of lamprey reticulospinal neurons: multiple distinct parameter sets yield realistic simulations.

Ruffolo JA, McClellan AD. Ruffolo JA, et al. J Neurophysiol. 2020 Sep 1;124(3):895-913. doi: 10.1152/jn.00070.2020. Epub 2020 Jul 22. J Neurophysiol. 2020. PMID: 32697608 Free article.

3

Designing proteins with language models.

Ruffolo JA, Madani A. Ruffolo JA, et al. Nat Biotechnol. 2024 Feb;42(2):200-202. doi: 10.1038/s41587-024-02123-4. Nat Biotechnol. 2024. PMID: 38361067 Review. No abstract available.

4

Geometric potentials from deep learning improve prediction of CDR H3 loop structures.

Ruffolo JA, Guerra C, Mahajan SP, Sulam J, Gray JJ. Ruffolo JA, et al. Bioinformatics. 2020 Jul 1;36(Suppl_1):i268-i275. doi: 10.1093/bioinformatics/btaa457. Bioinformatics. 2020. PMID: 32657412 Free PMC article.

5

Antibody structure prediction using interpretable deep learning.

Ruffolo JA, Sulam J, Gray JJ. Ruffolo JA, et al. Patterns (N Y). 2021 Dec 9;3(2):100406. doi: 10.1016/j.patter.2021.100406. eCollection 2022 Feb 11. Patterns (N Y). 2021. PMID: 35199061 Free PMC article.

6

Simultaneous prediction of antibody backbone and side-chain conformations with deep learning.

Akpinaroglu D, Ruffolo JA, Mahajan SP, Gray JJ. Akpinaroglu D, et al. Among authors: ruffolo ja. PLoS One. 2022 Jun 15;17(6):e0258173. doi: 10.1371/journal.pone.0258173. eCollection 2022. PLoS One. 2022. PMID: 35704640 Free PMC article.

7

Hallucinating structure-conditioned antibody libraries for target-specific binders.

Mahajan SP, Ruffolo JA, Frick R, Gray JJ. Mahajan SP, et al. Among authors: ruffolo ja. Front Immunol. 2022 Oct 21;13:999034. doi: 10.3389/fimmu.2022.999034. eCollection 2022. Front Immunol. 2022. PMID: 36341416 Free PMC article.

8

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

Chu LS, Ruffolo JA, Harmalkar A, Gray JJ. Chu LS, et al. Among authors: ruffolo ja. bioRxiv [Preprint]. 2023 Jul 1:2023.06.29.547134. doi: 10.1101/2023.06.29.547134. bioRxiv. 2023. Update in: Protein Sci. 2024 Feb;33(2):e4862. doi: 10.1002/pro.4862 PMID: 37425754 Free PMC article. Updated. Preprint.

9

Contextual protein and antibody encodings from equivariant graph transformers.

Mahajan SP, Ruffolo JA, Gray JJ. Mahajan SP, et al. Among authors: ruffolo ja. bioRxiv [Preprint]. 2023 Jul 29:2023.07.15.549154. doi: 10.1101/2023.07.15.549154. bioRxiv. 2023. PMID: 37503113 Free PMC article. Preprint.

10

IgLM: Infilling language modeling for antibody sequence design.

Shuai RW, Ruffolo JA, Gray JJ. Shuai RW, et al. Among authors: ruffolo ja. Cell Syst. 2023 Nov 15;14(11):979-989.e4. doi: 10.1016/j.cels.2023.10.001. Epub 2023 Oct 30. Cell Syst. 2023. PMID: 37909045 Free PMC article.

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