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Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.

Proteins

Kumar A, Campitelli P, Thorpe MF, Ozkan SB.
PMID: 26476100
Proteins. 2015 Dec;83(12):2279-92. doi: 10.1002/prot.24947. Epub 2015 Nov 17.

The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a...

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Kumar A, Campitelli P, Thorpe MF, et al. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins. 2015;83(12):2279-92doi: 10.1002/prot.24947.
Kumar, A., Campitelli, P., Thorpe, M. F., & Ozkan, S. B. (2015). Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins, 83(12), 2279-92. https://doi.org/10.1002/prot.24947
Kumar, Avishek, et al. "Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics." Proteins vol. 83,12 (2015): 2279-92. doi: https://doi.org/10.1002/prot.24947
Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins. 2015 Dec;83(12):2279-92. doi: 10.1002/prot.24947. Epub 2015 Nov 17. PMID: 26476100; PMCID: PMC4856442.
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Protein Misfolding and Endoplasmic Reticulum Stress in Chronic Lung Disease: Will Cell-Specific Targeting Be the Key to the Cure?.

Chest

Naiel S, Tat V, Padwal M, Vierhout M, Mekhael O, Yousof T, Ayoub A, Abed S, Dvorkin-Gheva A, Ask K.
PMID: 31778676
Chest. 2020 May;157(5):1207-1220. doi: 10.1016/j.chest.2019.11.009. Epub 2019 Nov 26.

Chronic lung disease accounts for a significant global burden with respect to death, disability, and health-care costs. Due to the heterogeneous nature and limited treatment options for these diseases, it is imperative that the cellular and molecular mechanisms underlying...

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Naiel S, Tat V, Padwal M, et al. Protein Misfolding and Endoplasmic Reticulum Stress in Chronic Lung Disease: Will Cell-Specific Targeting Be the Key to the Cure?. Chest. 2019;157(5):1207-1220doi: 10.1016/j.chest.2019.11.009.
Naiel, S., Tat, V., Padwal, M., Vierhout, M., Mekhael, O., Yousof, T., Ayoub, A., Abed, S., Dvorkin-Gheva, A., & Ask, K. (2020). Protein Misfolding and Endoplasmic Reticulum Stress in Chronic Lung Disease: Will Cell-Specific Targeting Be the Key to the Cure?. Chest, 157(5), 1207-1220. https://doi.org/10.1016/j.chest.2019.11.009
Naiel, Safaa, et al. "Protein Misfolding and Endoplasmic Reticulum Stress in Chronic Lung Disease: Will Cell-Specific Targeting Be the Key to the Cure?." Chest vol. 157,5 (2020): 1207-1220. doi: https://doi.org/10.1016/j.chest.2019.11.009
Naiel S, Tat V, Padwal M, Vierhout M, Mekhael O, Yousof T, Ayoub A, Abed S, Dvorkin-Gheva A, Ask K. Protein Misfolding and Endoplasmic Reticulum Stress in Chronic Lung Disease: Will Cell-Specific Targeting Be the Key to the Cure?. Chest. 2020 May;157(5):1207-1220. doi: 10.1016/j.chest.2019.11.009. Epub 2019 Nov 26. PMID: 31778676.
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Exploring early stages of the chemical unfolding of proteins at the proteome scale.

PLoS computational biology

Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpí JL, Orozco M.
PMID: 24348236
PLoS Comput Biol. 2013;9(12):e1003393. doi: 10.1371/journal.pcbi.1003393. Epub 2013 Dec 12.

After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins...

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Candotti M, Pérez A, Ferrer-Costa C, et al. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS Comput Biol. 2013;9(12):e1003393doi: 10.1371/journal.pcbi.1003393.
Candotti, M., Pérez, A., Ferrer-Costa, C., Rueda, M., Meyer, T., Gelpí, J. L., & Orozco, M. (2013). Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS computational biology, 9(12), e1003393. https://doi.org/10.1371/journal.pcbi.1003393
Candotti, Michela, et al. "Exploring early stages of the chemical unfolding of proteins at the proteome scale." PLoS computational biology vol. 9,12 (2013): e1003393. doi: https://doi.org/10.1371/journal.pcbi.1003393
Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpí JL, Orozco M. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS Comput Biol. 2013;9(12):e1003393. doi: 10.1371/journal.pcbi.1003393. Epub 2013 Dec 12. PMID: 24348236; PMCID: PMC3861036.
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