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PyRETIS 3: Conquering rare and slow events without boundaries.
J Comput Chem. 2024 Jun 5;45(15):1224-1234. doi: 10.1002/jcc.27319. Epub 2024 Feb 12.
J Comput Chem. 2024.
PMID: 38345082
Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps.
Zhang DT, Baldauf L, Roet S, Lervik A, van Erp TS.
Zhang DT, et al. Among authors: roet s.
Proc Natl Acad Sci U S A. 2024 Feb 13;121(7):e2318731121. doi: 10.1073/pnas.2318731121. Epub 2024 Feb 5.
Proc Natl Acad Sci U S A. 2024.
PMID: 38315841
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Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms.
Chaillet ML, van der Schot G, Gubins I, Roet S, Veltkamp RC, Förster F.
Chaillet ML, et al. Among authors: roet s.
Int J Mol Sci. 2023 Aug 29;24(17):13375. doi: 10.3390/ijms241713375.
Int J Mol Sci. 2023.
PMID: 37686180
Free PMC article.
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Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.
Roet S, Hooft F, Bolhuis PG, Swenson DWH, Vreede J.
Roet S, et al.
J Phys Chem B. 2022 Dec 8;126(48):10034-10044. doi: 10.1021/acs.jpcb.2c06235. Epub 2022 Nov 25.
J Phys Chem B. 2022.
PMID: 36427204
Free PMC article.
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Exchanging Replicas with Unequal Cost, Infinitely and Permanently.
Roet S, Zhang DT, van Erp TS.
Roet S, et al.
J Phys Chem A. 2022 Dec 1;126(47):8878-8886. doi: 10.1021/acs.jpca.2c06004. Epub 2022 Nov 17.
J Phys Chem A. 2022.
PMID: 36394633
Free PMC article.
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A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations.
Mons E, Roet S, Kim RQ, Mulder MPC.
Mons E, et al. Among authors: roet s.
Curr Protoc. 2022 Jun;2(6):e419. doi: 10.1002/cpz1.419.
Curr Protoc. 2022.
PMID: 35671150
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Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning.
Roet S, Daub CD, Riccardi E.
Roet S, et al.
J Chem Theory Comput. 2021 Oct 12;17(10):6193-6202. doi: 10.1021/acs.jctc.1c00458. Epub 2021 Sep 24.
J Chem Theory Comput. 2021.
PMID: 34555907
Free PMC article.
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PyRETIS 2: An improbability drive for rare events.
Riccardi E, Lervik A, Roet S, Aarøen O, van Erp TS.
Riccardi E, et al. Among authors: roet s.
J Comput Chem. 2020 Feb 5;41(4):370-377. doi: 10.1002/jcc.26112. Epub 2019 Nov 19.
J Comput Chem. 2020.
PMID: 31742744
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