Journal ArticleDOI
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric.
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In this article, the occurrence structures of nitrogenous bases and amino acids were studied and a structural metric which could measure the structure differences for bases or amino acids was devised to find the average distance matrices for them, respectively.Abstract:
COVID-19 pandemic has caused a global health crisis. Developing vaccines would need a good knowledge of genetic properties of SARS-CoV-2. The most fundamental approach is to look into the structures of its RNA, in particular, the nucleotides and amino acids. This motivates our research on this topic. We study the occurrence structures of nitrogenous bases and amino acids. To this aim, we devise a structural metric which could measure the structure differences for bases or amino acids. By analyzing various SARS-CoV-2 samples, we calculate the distance matrices for nitrogenous bases and amino acids. Based on the distance matrices, we find the average distance matrices for them, respectively. Then we identify the relations of all the minimal distances between bases and amino acids. The results also show that different substructures would yield much more diversified distances between amino acids. In the end, we also conduct the comparison of our structural metric with other frequently used metrics, in particular, Hausdorff metrics.read more
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References
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Journal ArticleDOI
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
David E. Gordon,Gwendolyn M. Jang,Mehdi Bouhaddou,Jiewei Xu,Kirsten Obernier,Kris M. White,Matthew J. O’Meara,Veronica V. Rezelj,Jeffrey Z. Guo,Danielle L. Swaney,Tia A. Tummino,Ruth Hüttenhain,Robyn M. Kaake,Alicia L. Richards,Beril Tutuncuoglu,Helene Foussard,Jyoti Batra,Kelsey M. Haas,Maya Modak,Minkyu Kim,Paige Haas,Benjamin J. Polacco,Hannes Braberg,Jacqueline M. Fabius,Manon Eckhardt,Margaret Soucheray,Melanie J. Bennett,Merve Cakir,Michael McGregor,Qiongyu Li,Bjoern Meyer,Ferdinand Roesch,Thomas Vallet,Alice Mac Kain,Lisa Miorin,Elena Moreno,Zun Zar Chi Naing,Yuan Zhou,Shiming Peng,Ying Shi,Ziyang Zhang,Wenqi Shen,Ilsa T Kirby,James E. Melnyk,John S. Chorba,Kevin Lou,Shizhong Dai,Inigo Barrio-Hernandez,Danish Memon,Claudia Hernandez-Armenta,Jiankun Lyu,Christopher J.P. Mathy,Tina Perica,Kala Bharath Pilla,Sai J. Ganesan,Daniel J. Saltzberg,Rakesh Ramachandran,Xi Liu,Sara Brin Rosenthal,Lorenzo Calviello,Srivats Venkataramanan,Jose Liboy-Lugo,Yizhu Lin,Xi Ping Huang,Yongfeng Liu,Stephanie A. Wankowicz,Markus Bohn,Maliheh Safari,Fatima S. Ugur,Cassandra Koh,Nastaran Sadat Savar,Quang Dinh Tran,Djoshkun Shengjuler,Sabrina J. Fletcher,Michael C. O’Neal,Yiming Cai,Jason C.J. Chang,David J. Broadhurst,Saker Klippsten,Phillip P. Sharp,Nicole A. Wenzell,Duygu Kuzuoğlu-Öztürk,Hao-Yuan Wang,Raphael Trenker,Janet M. Young,Devin A. Cavero,Devin A. Cavero,Joseph Hiatt,Joseph Hiatt,Theodore L. Roth,Ujjwal Rathore,Ujjwal Rathore,Advait Subramanian,Julia Noack,Mathieu Hubert,Robert M. Stroud,Alan D. Frankel,Oren S. Rosenberg,Kliment A. Verba,David A. Agard,Melanie Ott,Michael Emerman,Natalia Jura,Mark von Zastrow,Eric Verdin,Eric Verdin,Alan Ashworth,Olivier Schwartz,Christophe d'Enfert,Shaeri Mukherjee,Matthew P. Jacobson,Harmit S. Malik,Danica Galonić Fujimori,Trey Ideker,Charles S. Craik,Stephen N. Floor,James S. Fraser,John D. Gross,Andrej Sali,Bryan L. Roth,Davide Ruggero,Jack Taunton,Tanja Kortemme,Pedro Beltrao,Marco Vignuzzi,Adolfo García-Sastre,Kevan M. Shokat,Brian K. Shoichet,Nevan J. Krogan +128 more
TL;DR: A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
Journal ArticleDOI
A Contemporary View of Coronavirus Transcription
TL;DR: The hallmark of coronavirus transcription is the production of multiple subgenomic mRNAs that contain sequences corresponding to both ends of the genome.
Book ChapterDOI
Viral and Cellular mRNA Translation in Coronavirus-Infected Cells.
TL;DR: This chapter describes the current understanding of the mechanisms involved in coronavirus mRNA translation and changes in host mRNA translation observed in coronvirus-infected cells.
Journal ArticleDOI
SARS coronavirus replicase proteins in pathogenesis.
TL;DR: The evolution of the ORF1ab proteins may be determined as much by issues of host range and virulence as they are by specific requirements for intracellular replication.
Journal ArticleDOI
Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences
Tae-Kun Seo,Hirohisa Kishino +1 more
TL;DR: By analyzing divergent and conserved interspecific mammalian sequences and intraspecific human population data, the superiority of the codon substitution models is shown and the advantages and disadvantages of the models of the 3 types are discussed.