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Expulsion mechanism of the substrate-translocating subunit in ECF transporters.
Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Thangaratnarajah C, et al. Among authors: borges araujo l. Nat Commun. 2023 Jul 25;14(1):4484. doi: 10.1038/s41467-023-40266-1. Nat Commun. 2023. PMID: 37491368 Free PMC article.
Martini 3 Coarse-Grained Force Field for Cholesterol.
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Borges-Araújo L, et al. J Chem Theory Comput. 2023 Oct 24;19(20):7387-7404. doi: 10.1021/acs.jctc.3c00547. Epub 2023 Oct 5. J Chem Theory Comput. 2023. PMID: 37796943
Pragmatic Coarse-Graining of Proteins: Models and Applications.
Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Borges-Araújo L, et al. J Chem Theory Comput. 2023 Oct 24;19(20):7112-7135. doi: 10.1021/acs.jctc.3c00733. Epub 2023 Oct 3. J Chem Theory Comput. 2023. PMID: 37788237 Review.
Assessing the Martini 3 protein model: A review of its path and potential.
Borges-Araújo L, Pereira GP, Valério M, Souza PCT. Borges-Araújo L, et al. Biochim Biophys Acta Proteins Proteom. 2024 Jul 1;1872(4):141014. doi: 10.1016/j.bbapap.2024.141014. Epub 2024 Apr 25. Biochim Biophys Acta Proteins Proteom. 2024. PMID: 38670324 Review.
Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics.
Pereira GP, Alessandri R, Domínguez M, Araya-Osorio R, Grünewald L, Borges-Araújo L, Wu S, Marrink SJ, Souza PCT, Mera-Adasme R. Pereira GP, et al. Among authors: borges araujo l. J Chem Theory Comput. 2024 Jul 9;20(13):5763-5773. doi: 10.1021/acs.jctc.4c00275. Epub 2024 Jun 26. J Chem Theory Comput. 2024. PMID: 38924075
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