A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein

The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It...
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Autor*in:	Lianjie Zeng [verfasserIn] Yitan Lu [verfasserIn] Wenying Yan [verfasserIn] Yang Yang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	COVID-19 conservation co-conservation protein co-conservation weighted network spike protein

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 24(2023), 4, p 3255
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:4, p 3255

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms24043255

Katalog-ID:	DOAJ080263372

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520			\|a The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.
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allfields	10.3390/ijms24043255 doi (DE-627)DOAJ080263372 (DE-599)DOAJ3bbe95aa56c64921bafa8351028fcb85 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Lianjie Zeng verfasserin aut A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations. COVID-19 conservation co-conservation protein co-conservation weighted network spike protein Biology (General) Chemistry Yitan Lu verfasserin aut Wenying Yan verfasserin aut Yang Yang verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 4, p 3255 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:4, p 3255 https://doi.org/10.3390/ijms24043255 kostenfrei https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 kostenfrei https://www.mdpi.com/1422-0067/24/4/3255 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 4, p 3255
spelling	10.3390/ijms24043255 doi (DE-627)DOAJ080263372 (DE-599)DOAJ3bbe95aa56c64921bafa8351028fcb85 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Lianjie Zeng verfasserin aut A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations. COVID-19 conservation co-conservation protein co-conservation weighted network spike protein Biology (General) Chemistry Yitan Lu verfasserin aut Wenying Yan verfasserin aut Yang Yang verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 4, p 3255 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:4, p 3255 https://doi.org/10.3390/ijms24043255 kostenfrei https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 kostenfrei https://www.mdpi.com/1422-0067/24/4/3255 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 4, p 3255
allfields_unstemmed	10.3390/ijms24043255 doi (DE-627)DOAJ080263372 (DE-599)DOAJ3bbe95aa56c64921bafa8351028fcb85 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Lianjie Zeng verfasserin aut A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations. COVID-19 conservation co-conservation protein co-conservation weighted network spike protein Biology (General) Chemistry Yitan Lu verfasserin aut Wenying Yan verfasserin aut Yang Yang verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 4, p 3255 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:4, p 3255 https://doi.org/10.3390/ijms24043255 kostenfrei https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 kostenfrei https://www.mdpi.com/1422-0067/24/4/3255 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 4, p 3255
allfieldsGer	10.3390/ijms24043255 doi (DE-627)DOAJ080263372 (DE-599)DOAJ3bbe95aa56c64921bafa8351028fcb85 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Lianjie Zeng verfasserin aut A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations. COVID-19 conservation co-conservation protein co-conservation weighted network spike protein Biology (General) Chemistry Yitan Lu verfasserin aut Wenying Yan verfasserin aut Yang Yang verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 4, p 3255 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:4, p 3255 https://doi.org/10.3390/ijms24043255 kostenfrei https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 kostenfrei https://www.mdpi.com/1422-0067/24/4/3255 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 4, p 3255
allfieldsSound	10.3390/ijms24043255 doi (DE-627)DOAJ080263372 (DE-599)DOAJ3bbe95aa56c64921bafa8351028fcb85 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Lianjie Zeng verfasserin aut A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations. COVID-19 conservation co-conservation protein co-conservation weighted network spike protein Biology (General) Chemistry Yitan Lu verfasserin aut Wenying Yan verfasserin aut Yang Yang verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 4, p 3255 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:4, p 3255 https://doi.org/10.3390/ijms24043255 kostenfrei https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 kostenfrei https://www.mdpi.com/1422-0067/24/4/3255 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 4, p 3255
language	English
source	In International Journal of Molecular Sciences 24(2023), 4, p 3255 volume:24 year:2023 number:4, p 3255
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container_title	International Journal of Molecular Sciences
authorswithroles_txt_mv	Lianjie Zeng @@aut@@ Yitan Lu @@aut@@ Wenying Yan @@aut@@ Yang Yang @@aut@@
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callnumber-first	Q - Science
author	Lianjie Zeng
spellingShingle	Lianjie Zeng misc QH301-705.5 misc QD1-999 misc COVID-19 misc conservation misc co-conservation misc protein co-conservation weighted network misc spike protein misc Biology (General) misc Chemistry A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein
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topic_title	QH301-705.5 QD1-999 A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein COVID-19 conservation co-conservation protein co-conservation weighted network spike protein
topic	misc QH301-705.5 misc QD1-999 misc COVID-19 misc conservation misc co-conservation misc protein co-conservation weighted network misc spike protein misc Biology (General) misc Chemistry
topic_unstemmed	misc QH301-705.5 misc QD1-999 misc COVID-19 misc conservation misc co-conservation misc protein co-conservation weighted network misc spike protein misc Biology (General) misc Chemistry
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title	A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein
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title_full	A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein
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title_sort	protein co-conservation network model characterizes mutation effects on sars-cov-2 spike protein
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title_auth	A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein
abstract	The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.
abstractGer	The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.
abstract_unstemmed	The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors’ degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.
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container_issue	4, p 3255
title_short	A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein
url	https://doi.org/10.3390/ijms24043255 https://doaj.org/article/3bbe95aa56c64921bafa8351028fcb85 https://www.mdpi.com/1422-0067/24/4/3255 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067
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