Ytreberg FM - 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: ytreberg fm. Sci Rep. 2024 Oct 4;14(1):23122. doi: 10.1038/s41598-024-72491-z. Sci Rep. 2024. PMID: 39366988 Free PMC article.

2

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

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

3

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: ytreberg fm. 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.

4

Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein.

Beach SS, Hull MA, Ytreberg FM, Patel JS, Miura TA. Beach SS, et al. Among authors: ytreberg fm. J Virol. 2022 Jul 13;96(13):e0035322. doi: 10.1128/jvi.00353-22. Epub 2022 Jun 9. J Virol. 2022. PMID: 35678603 Free PMC article.

5

The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6.

Barnes JE, Lund-Andersen PK, Patel JS, Ytreberg FM. Barnes JE, et al. Among authors: ytreberg fm. Sci Rep. 2022 Nov 5;12(1):18819. doi: 10.1038/s41598-022-23482-5. Sci Rep. 2022. PMID: 36335244 Free PMC article.

6

Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability.

Sapozhnikov Y, Patel JS, Ytreberg FM, Miller CR. Sapozhnikov Y, et al. Among authors: ytreberg fm. BMC Bioinformatics. 2023 Nov 12;24(1):426. doi: 10.1186/s12859-023-05537-0. BMC Bioinformatics. 2023. PMID: 37953256 Free PMC article.

7

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

Chi LA, Barnes JE, Suresh Patel J, Ytreberg FM. Chi LA, et al. Among authors: ytreberg fm. bioRxiv [Preprint]. 2024 May 22:2024.05.22.595230. doi: 10.1101/2024.05.22.595230. bioRxiv. 2024. Update in: Sci Rep. 2024 Oct 4;14(1):23122. doi: 10.1038/s41598-024-72491-z PMID: 38826284 Free PMC article. Updated. Preprint.

8

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

Patel JS, Ytreberg FM. Patel JS, et al. Among authors: ytreberg fm. 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.

9

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: ytreberg fm. PLoS One. 2020 May 29;15(5):e0233509. doi: 10.1371/journal.pone.0233509. eCollection 2020. PLoS One. 2020. PMID: 32470971 Free PMC article.

10

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: ytreberg fm. PLoS One. 2020 Dec 21;15(12):e0240573. doi: 10.1371/journal.pone.0240573. eCollection 2020. PLoS One. 2020. PMID: 33347442 Free PMC article.

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