Patel JS - Search Results

1

Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data.

Chi LA, Barnes JE, Patel JS, Ytreberg FM. Chi LA, et al. Among authors: patel js. Sci Rep. 2024 Oct 4;14(1):23122. doi: 10.1038/s41598-024-72491-z. Sci Rep. 2024. PMID: 39366988 Free PMC article.

2

Fast Calculation of Protein-Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model.

Patel JS, Ytreberg FM. Patel JS, et al. J Chem Theory Comput. 2018 Feb 13;14(2):991-997. doi: 10.1021/acs.jctc.7b00660. Epub 2018 Jan 16. J Chem Theory Comput. 2018. PMID: 29286646 Free PMC article.

3

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations.

Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL. Patel JS, et al. PLoS Comput Biol. 2018 Jan 24;14(1):e1005974. doi: 10.1371/journal.pcbi.1005974. eCollection 2018 Jan. PLoS Comput Biol. 2018. PMID: 29364888 Free PMC article.

4

Expanding the watch list for potential Ebola virus antibody escape mutations.

Patel JS, Quates CJ, Johnson EL, Ytreberg FM. Patel JS, et al. PLoS One. 2019 Mar 21;14(3):e0211093. doi: 10.1371/journal.pone.0211093. eCollection 2019. PLoS One. 2019. PMID: 30897171 Free PMC article.

5

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness.

Yang J, Naik N, Patel JS, Wylie CS, Gu W, Huang J, Ytreberg FM, Naik MT, Weinreich DM, Rubenstein BM. Yang J, et al. Among authors: patel js. PLoS One. 2020 May 29;15(5):e0233509. doi: 10.1371/journal.pone.0233509. eCollection 2020. PLoS One. 2020. PMID: 32470971 Free PMC article.

6

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance.

Patel D, Barnes JE, Davies WIL, Stenkamp DL, Patel JS. Patel D, et al. Among authors: patel js. PLoS Comput Biol. 2020 Oct 21;16(10):e1008212. doi: 10.1371/journal.pcbi.1008212. eCollection 2020 Oct. PLoS Comput Biol. 2020. PMID: 33085657 Free PMC article.

7

Assessment of software methods for estimating protein-protein relative binding affinities.

Gonzalez TR, Martin KP, Barnes JE, Patel JS, Ytreberg FM. Gonzalez TR, et al. Among authors: patel js. PLoS One. 2020 Dec 21;15(12):e0240573. doi: 10.1371/journal.pone.0240573. eCollection 2020. PLoS One. 2020. PMID: 33347442 Free PMC article.

8

Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.

Patel D, Patel JS, Ytreberg FM. Patel D, et al. Among authors: patel js. J Chem Theory Comput. 2021 Apr 13;17(4):2457-2464. doi: 10.1021/acs.jctc.0c01045. Epub 2021 Mar 12. J Chem Theory Comput. 2021. PMID: 33709712 Free PMC article.

9

EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde.

Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, Marx CJ. Bazurto JV, et al. Among authors: patel js. PLoS Biol. 2021 May 26;19(5):e3001208. doi: 10.1371/journal.pbio.3001208. eCollection 2021 May. PLoS Biol. 2021. PMID: 34038406 Free PMC article.

10

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin.

Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT. Patel D, et al. Among authors: patel js. J Chem Inf Model. 2022 Mar 14;62(5):1282-1293. doi: 10.1021/acs.jcim.1c01104. Epub 2022 Feb 23. J Chem Inf Model. 2022. PMID: 35194993 Free PMC article.

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