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Part 1: Document Description
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Citation |
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Title: |
Additional files for: Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. |
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Identification Number: |
doi:10.21979/N9/TQEOP6 |
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Distributor: |
DR-NTU (Data) |
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Date of Distribution: |
2019-03-22 |
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Version: |
1 |
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Bibliographic Citation: |
Zhou, Xinrui; Zheng, Jie; Ivan, Fransiskus Xaverius; Yin, Rui; Shoba Ranganathan; Chow, Vincent T. K.; Kwoh, Chee-Keong, 2019, "Additional files for: Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.", https://doi.org/10.21979/N9/TQEOP6, DR-NTU (Data), V1 |
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Citation |
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Title: |
Additional files for: Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. |
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Identification Number: |
doi:10.21979/N9/TQEOP6 |
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Authoring Entity: |
Zhou, Xinrui (Nanyang Technological University) |
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Zheng, Jie (Nanyang Technological University) |
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Ivan, Fransiskus Xaverius (Nanyang Technological University) |
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Yin, Rui (Nanyang Technological University) |
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Shoba Ranganathan (Nanyang Technological University) |
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Chow, Vincent T. K. (Nanyang Technological University) |
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Kwoh, Chee-Keong (Nanyang Technological University) |
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Software used in Production: |
Adobe reader |
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Grant Number: |
Academic Research Fund Tier 1 grant MOE2014-T2-2-023 |
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Distributor: |
DR-NTU (Data) |
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Access Authority: |
Zhou Xinrui |
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Depositor: |
Zhou Xinrui |
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Date of Deposit: |
2019-03-22 |
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Holdings Information: |
https://doi.org/10.21979/N9/TQEOP6 |
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Study Scope |
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Keywords: |
Computer and Information Science, Medicine, Health and Life Sciences, Computer and Information Science, Medicine, Health and Life Sciences, Influenza viruses, receptor binding specificity, Influenza A/H7N9, Host specificity, Molecular docking, Molecular dynamics simulation, Receptor binding |
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Abstract: |
BACKGROUND:<br> Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013 and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several hosts and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. <br><br> RESULTS:<br> The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. <br><br> CONCLUSION:<br> The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses. |
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Kind of Data: |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Identification Number: |
10.1186/s12864-018-4461-z |
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Bibliographic Citation: |
Zhou, X., Zheng, J., Ivan, F. X., Yin, R., Ranganathan, S., Chow, V. T., & Kwoh, C. K. (2018). Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. BMC genomics, 19(2), 41-50. |
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Citation |
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Identification Number: |
10356/84227 |
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Bibliographic Citation: |
Zhou, X., Zheng, J., Ivan, F. X., Yin, R., Ranganathan, S., Chow, V. T., & Kwoh, C. K. (2018). Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. BMC genomics, 19(2), 41-50. |
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Label: |
Additional file 1.pdf |
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Text: |
Phylogenetic trees of influenza A/H7N9. Time scale phylogenetic trees of PB2, PB1, PA, HA, NP, NA, M1 and NS1 genes of influenza H7N9 strain. |
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Notes: |
application/pdf |
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Label: |
Additional file 2.pdf |
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Text: |
Superimpose the best and worst docked HA-ligand complexes. Visualize the structure of docked SH13-LSTa, SH13-LSTc, TW17-LSTa and TW17-LSTc complexes with the highest and the lowest binding affinities. |
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Notes: |
application/pdf |
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Label: |
Additional file 3.pdf |
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Text: |
VdW energy, electrostatic energy and total interaction energy of SH13-LSTa, SH13-LSTc, TW17-LSTa and TW17-LSTc during the whole simulation (50 ns). |
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Notes: |
application/pdf |
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Label: |
Additional file 4.pdf |
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Text: |
Two rounds of 50 ns molecular dynamics simulation for SH13-LSTa, SH13-LSTc, TW17-LSTa, TW17-LSTc |
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Notes: |
application/pdf |
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Label: |
Additional file 5.pdf |
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Residue contributions during the whole simulation process. |
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Notes: |
application/pdf |
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Label: |
Additional file 6.pdf |
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Text: |
Average energy contribution of residues that involved in receptorligand interactions in the optimally docked complexes |
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Notes: |
application/pdf |