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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. Among authors: souza pct. 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.
Computational Modeling of Realistic Cell Membranes.
Marrink SJ, Corradi V, Souza PCT, Ingólfsson HI, Tieleman DP, Sansom MSP. Marrink SJ, et al. Among authors: souza pct. Chem Rev. 2019 May 8;119(9):6184-6226. doi: 10.1021/acs.chemrev.8b00460. Epub 2019 Jan 9. Chem Rev. 2019. PMID: 30623647 Free PMC article. Review.
A Practical View of the Martini Force Field.
Bruininks BMH, Souza PCT, Marrink SJ. Bruininks BMH, et al. Among authors: souza pct. Methods Mol Biol. 2019;2022:105-127. doi: 10.1007/978-1-4939-9608-7_5. Methods Mol Biol. 2019. PMID: 31396901
Pitfalls of the Martini Model.
Alessandri R, Souza PCT, Thallmair S, Melo MN, de Vries AH, Marrink SJ. Alessandri R, et al. Among authors: souza pct. J Chem Theory Comput. 2019 Oct 8;15(10):5448-5460. doi: 10.1021/acs.jctc.9b00473. Epub 2019 Sep 24. J Chem Theory Comput. 2019. PMID: 31498621 Free PMC article.
Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field.
Khan HM, Souza PCT, Thallmair S, Barnoud J, de Vries AH, Marrink SJ, Reuter N. Khan HM, et al. Among authors: souza pct. J Chem Theory Comput. 2020 Apr 14;16(4):2550-2560. doi: 10.1021/acs.jctc.9b01194. Epub 2020 Mar 9. J Chem Theory Comput. 2020. PMID: 32096995 Free PMC article.
Titratable Martini model for constant pH simulations.
Grünewald F, Souza PCT, Abdizadeh H, Barnoud J, de Vries AH, Marrink SJ. Grünewald F, et al. Among authors: souza pct. J Chem Phys. 2020 Jul 14;153(2):024118. doi: 10.1063/5.0014258. J Chem Phys. 2020. PMID: 32668918
50 results