Chakravarty D - Search Results

1

AlphaFold2 has more to learn about protein energy landscapes.

Chakravarty D, Schafer JW, Chen EA, Thole JR, Porter LL. Chakravarty D, et al. bioRxiv [Preprint]. 2023 Dec 13:2023.12.12.571380. doi: 10.1101/2023.12.12.571380. bioRxiv. 2023. Update in: Nat Commun. 2024 Aug 24;15(1):7296. doi: 10.1038/s41467-024-51801-z PMID: 38168383 Free PMC article. Updated. Preprint.

2

Distinguishing features of fold-switching proteins.

Chakravarty D, Schafer JW, Porter LL. Chakravarty D, et al. Protein Sci. 2023 Mar;32(3):e4596. doi: 10.1002/pro.4596. Protein Sci. 2023. PMID: 36782353 Free PMC article. Review.

3

Identification of a covert evolutionary pathway between two protein folds.

Chakravarty D, Sreenivasan S, Swint-Kruse L, Porter LL. Chakravarty D, et al. Nat Commun. 2023 Jun 1;14(1):3177. doi: 10.1038/s41467-023-38519-0. Nat Commun. 2023. PMID: 37264049 Free PMC article.

4

ColabFold predicts alternative protein structures from single sequences, coevolution unnecessary for AF-cluster.

Porter LL, Chakravarty D, Schafer JW, Chen EA. Porter LL, et al. Among authors: chakravarty d. bioRxiv [Preprint]. 2023 Nov 25:2023.11.21.567977. doi: 10.1101/2023.11.21.567977. bioRxiv. 2023. PMID: 38076792 Free PMC article. Preprint.

5

Sequence clustering confounds AlphaFold2.

Schafer JW, Chakravarty D, Chen EA, Porter LL. Schafer JW, et al. Among authors: chakravarty d. bioRxiv [Preprint]. 2024 Jan 9:2024.01.05.574434. doi: 10.1101/2024.01.05.574434. bioRxiv. 2024. PMID: 38313252 Free PMC article. Preprint.

6

AlphaFold predictions of fold-switched conformations are driven by structure memorization.

Chakravarty D, Schafer JW, Chen EA, Thole JF, Ronish LA, Lee M, Porter LL. Chakravarty D, et al. Nat Commun. 2024 Aug 24;15(1):7296. doi: 10.1038/s41467-024-51801-z. Nat Commun. 2024. PMID: 39181864 Free PMC article.

7

Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction.

Chakravarty D, Lee M, Porter LL. Chakravarty D, et al. Curr Opin Struct Biol. 2025 Jan 4;90:102973. doi: 10.1016/j.sbi.2024.102973. Online ahead of print. Curr Opin Struct Biol. 2025. PMID: 39756261 Free article. Review.

8

Genetic Ancestry-Based Differences in Biomarker-Based Eligibility for Precision Oncology Therapies.

Arora K, Suehnholz SP, Zhang H, Ostrovnaya I, Kundra R, Nandakumar S, Nissan MH, Brannon AR, Bandlamudi C, Ladanyi M, Drilon A, Brown CL, Solit DB, Schultz N, Berger MF, Chakravarty D. Arora K, et al. Among authors: chakravarty d. JAMA Oncol. 2025 Jan 9. doi: 10.1001/jamaoncol.2024.5794. Online ahead of print. JAMA Oncol. 2025. PMID: 39786754

9

Clinicogenomic landscape of pancreatic adenocarcinoma identifies KRAS mutant dosage as prognostic of overall survival.

Varghese AM, Perry MA, Chou JF, Nandakumar S, Muldoon D, Erakky A, Zucker A, Fong C, Mehine M, Nguyen B, Basturk O, Balogun F, Kelsen DP, Brannon AR, Mandelker D, Vakiani E, Park W, Yu KH, Stadler ZK, Schattner MA, Jarnagin WR, Wei AC, Chakravarty D, Capanu M, Schultz N, Berger MF, Iacobuzio-Donahue CA, Bandlamudi C, O'Reilly EM. Varghese AM, et al. Among authors: chakravarty d. Nat Med. 2025 Jan 3. doi: 10.1038/s41591-024-03362-3. Online ahead of print. Nat Med. 2025. PMID: 39753968

10

Acceptability and feasibility of a urine-based tenofovir adherence assay for monitoring and providing feedback on PrEP adherence in Kenya.

Okello P, Velloza J, Ogello V, Owidi E, Mogere P, Gakuo S, Chakravarty D, Biwott C, Chatterjee P, Mugo N, Gandhi M, Ngure K. Okello P, et al. Among authors: chakravarty d. AIDS Care. 2024 Dec 28:1-13. doi: 10.1080/09540121.2024.2444556. Online ahead of print. AIDS Care. 2024. PMID: 39733245

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