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Resolving the fine structure in the energy landscapes of repeat proteins.
QRB Discov. 2022 Jun 10;3:e7. doi: 10.1017/qrd.2022.4. eCollection 2022.
QRB Discov. 2022.
PMID: 37529289
Free PMC article.
Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method.
Sanches MN, Knapp K, Oliveira AB Jr, Wolynes PG, Onuchic JN, Leite VBP.
Sanches MN, et al. Among authors: oliveira ab jr.
J Phys Chem B. 2022 Jan 13;126(1):93-99. doi: 10.1021/acs.jpcb.1c08525. Epub 2021 Dec 30.
J Phys Chem B. 2022.
PMID: 34968059
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SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC.
de Oliveira AB Jr, et al.
Protein Sci. 2022 Jan;31(1):158-172. doi: 10.1002/pro.4209. Epub 2021 Nov 1.
Protein Sci. 2022.
PMID: 34655449
Free PMC article.
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Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m7GTP cap recognition.
Hernández-Alvarez L, Oliveira AB Jr, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP.
Hernández-Alvarez L, et al. Among authors: oliveira ab jr.
Comput Struct Biotechnol J. 2021 Apr 5;19:2027-2044. doi: 10.1016/j.csbj.2021.03.036. eCollection 2021.
Comput Struct Biotechnol J. 2021.
PMID: 33995900
Free PMC article.
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pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study.
de Oliveira VM, Caetano DLZ, da Silva FB, Mouro PR, de Oliveira AB Jr, de Carvalho SJ, Leite VBP.
de Oliveira VM, et al. Among authors: de oliveira ab jr.
J Chem Theory Comput. 2020 Jan 14;16(1):765-772. doi: 10.1021/acs.jctc.9b00894. Epub 2019 Dec 6.
J Chem Theory Comput. 2020.
PMID: 31756296
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Distinguishing Biomolecular Pathways and Metastable States.
Oliveira AB Jr, Yang H, Whitford PC, Leite VBP.
Oliveira AB Jr, et al.
J Chem Theory Comput. 2019 Nov 12;15(11):6482-6490. doi: 10.1021/acs.jctc.9b00704. Epub 2019 Nov 1.
J Chem Theory Comput. 2019.
PMID: 31618581
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Visualization of protein folding funnels in lattice models.
Oliveira AB Jr, Fatore FM, Paulovich FV, Oliveira ON Jr, Leite VB.
Oliveira AB Jr, et al.
PLoS One. 2014 Jul 10;9(7):e100861. doi: 10.1371/journal.pone.0100861. eCollection 2014.
PLoS One. 2014.
PMID: 25010343
Free PMC article.
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