Poma AB - Search Results

1

Polysaccharide-Protein Complexes in a Coarse-Grained Model.

Poma AB, Chwastyk M, Cieplak M. Poma AB, et al. J Phys Chem B. 2015 Sep 10;119(36):12028-41. doi: 10.1021/acs.jpcb.5b06141. Epub 2015 Aug 26. J Phys Chem B. 2015. PMID: 26291477

2

Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins.

Poma AB, Cieplak M, Theodorakis PE. Poma AB, et al. J Chem Theory Comput. 2017 Mar 14;13(3):1366-1374. doi: 10.1021/acs.jctc.6b00986. Epub 2017 Feb 24. J Chem Theory Comput. 2017. PMID: 28195464 Free article.

3

Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids.

Poma AB, Chwastyk M, Cieplak M. Poma AB, et al. Phys Chem Chem Phys. 2017 Oct 25;19(41):28195-28206. doi: 10.1039/c7cp05269c. Phys Chem Chem Phys. 2017. PMID: 29022971

4

Generalization of the elastic network model for the study of large conformational changes in biomolecules.

Poma AB , Li MS , Theodorakis PE . Poma AB , et al. Phys Chem Chem Phys. 2018 Jun 27;20(25):17020-17028. doi: 10.1039/c8cp03086c. Phys Chem Chem Phys. 2018. PMID: 29904772

5

Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes.

Senapati S, Poma AB, Cieplak M, Filipek S, Park PSH. Senapati S, et al. Among authors: poma ab. Anal Chem. 2019 Jun 4;91(11):7226-7235. doi: 10.1021/acs.analchem.9b00546. Epub 2019 May 16. Anal Chem. 2019. PMID: 31074606 Free PMC article.

6

Quantitative determination of mechanical stability in the novel coronavirus spike protein.

Moreira RA , Chwastyk M , Baker JL , Guzman HV , Poma AB . Moreira RA , et al. Among authors: poma ab. Nanoscale. 2020 Aug 21;12(31):16409-16413. doi: 10.1039/d0nr03969a. Epub 2020 Jul 29. Nanoscale. 2020. PMID: 32725017

7

Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.

Mahmood MI, Poma AB, Okazaki KI. Mahmood MI, et al. Among authors: poma ab. Front Mol Biosci. 2021 Feb 22;8:619381. doi: 10.3389/fmolb.2021.619381. eCollection 2021. Front Mol Biosci. 2021. PMID: 33693028 Free PMC article.

8

Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations.

Poma AB, Thu TTM, Tri LTM, Nguyen HL, Li MS. Poma AB, et al. J Phys Chem B. 2021 Jul 22;125(28):7628-7637. doi: 10.1021/acs.jpcb.1c02322. Epub 2021 Jul 12. J Phys Chem B. 2021. PMID: 34253022 Free PMC article.

9

Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations.

Cofas-Vargas LF, Olivos-Ramirez GE, Chwastyk M, Moreira RA, Baker JL, Marrink SJ, Poma AB. Cofas-Vargas LF, et al. Among authors: poma ab. Nanoscale. 2024 Oct 17;16(40):18824-18834. doi: 10.1039/d4nr02074j. Nanoscale. 2024. PMID: 39351797

10

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies.

Poma AB, Guzman HV, Li MS, Theodorakis PE. Poma AB, et al. Beilstein J Nanotechnol. 2019 Feb 19;10:500-513. doi: 10.3762/bjnano.10.51. eCollection 2019. Beilstein J Nanotechnol. 2019. PMID: 30873322 Free PMC article.

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