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Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations.
Swier LJYM, Monjas L, Reeßing F, Oudshoorn RC, Aisyah, Primke T, Bakker MM, van Olst E, Ritschel T, Faustino I, Marrink SJ, Hirsch AKH, Slotboom DJ. Swier LJYM, et al. Among authors: faustino i. Medchemcomm. 2017 Mar 31;8(5):1121-1130. doi: 10.1039/c7md00079k. eCollection 2017 May 1. Medchemcomm. 2017. PMID: 30108823 Free PMC article.
Martini 3: a general purpose force field for coarse-grained molecular dynamics.
Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, Domański J, Javanainen M, Martinez-Seara H, Reuter N, Best RB, Vattulainen I, Monticelli L, Periole X, Tieleman DP, de Vries AH, Marrink SJ. Souza PCT, et al. Among authors: faustino i. Nat Methods. 2021 Apr;18(4):382-388. doi: 10.1038/s41592-021-01098-3. Epub 2021 Mar 29. Nat Methods. 2021. PMID: 33782607
Martini Coarse-Grained Force Field: Extension to RNA.
Uusitalo JJ, Ingólfsson HI, Marrink SJ, Faustino I. Uusitalo JJ, et al. Among authors: faustino i. Biophys J. 2017 Jul 25;113(2):246-256. doi: 10.1016/j.bpj.2017.05.043. Epub 2017 Jun 17. Biophys J. 2017. PMID: 28633759 Free PMC article.
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.
Faustino I, Marrink SJ. Faustino I, et al. Bioinformatics. 2017 Dec 1;33(23):3813-3815. doi: 10.1093/bioinformatics/btx444. Bioinformatics. 2017. PMID: 29036584
A tutorial on the use and application is also available at http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna. CONTACT: i.faustino@rug.nl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
A tutorial on the use and application is also available at http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna …
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes.
Garcia-Lopez A, Tessaro F, Jonker HRA, Wacker A, Richter C, Comte A, Berntenis N, Schmucki R, Hatje K, Petermann O, Chiriano G, Perozzo R, Sciarra D, Konieczny P, Faustino I, Fournet G, Orozco M, Artero R, Metzger F, Ebeling M, Goekjian P, Joseph B, Schwalbe H, Scapozza L. Garcia-Lopez A, et al. Among authors: faustino i. Nat Commun. 2018 May 23;9(1):2032. doi: 10.1038/s41467-018-04110-1. Nat Commun. 2018. PMID: 29795225 Free PMC article.
Parmbsc1: a refined force field for DNA simulations.
Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí JL, González C, Vendruscolo M, Laughton CA, Harris SA, Case DA, Orozco M. Ivani I, et al. Among authors: faustino i. Nat Methods. 2016 Jan;13(1):55-8. doi: 10.1038/nmeth.3658. Epub 2015 Nov 16. Nat Methods. 2016. PMID: 26569599 Free PMC article.
Photoswitching of DNA Hybridization Using a Molecular Motor.
Lubbe AS, Liu Q, Smith SJ, de Vries JW, Kistemaker JCM, de Vries AH, Faustino I, Meng Z, Szymanski W, Herrmann A, Feringa BL. Lubbe AS, et al. Among authors: faustino i. J Am Chem Soc. 2018 Apr 18;140(15):5069-5076. doi: 10.1021/jacs.7b09476. Epub 2018 Apr 10. J Am Chem Soc. 2018. PMID: 29551069 Free PMC article.
54 results