Predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein

Keywords

Biology, Spike Protein, Spike (software development), Coronavirus, Computational biology

References

• Ecology, evolution and classification of bat coronaviruses in the aftermath of SARSFrançois Bry, Tim Furche, Alina Hang — 2013
• DISOPRED3: precise disordered region predictions with annotated protein-binding activityNeil Leach — 2014
• Human intestine luminal ACE2 and amino acid transporter expression increased by ACE-inhibitors泰明 西田 — 2014
• An Update on the Tissue Renin Angiotensin System and Its Role in Physiology and PathologyLynda M. Applegate, David E. Bell, Michael Norris — 2019
• The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, ChinaD. Hui, Esam I Azhar, T. Madani — 2020
• Protein disorder and the evolution of molecular recognition: theory, predictions and observations.A. Keith Dunker, Ethan C. Garner, S Guilliot — 1998
• Coronaviruses: An Overview of Their Replication and PathogenesisAnthony R. Fehr, Stanley Perlman — 2015
• Middle East Respiratory Syndrome Coronavirus (MERS-CoV): A Perpetual ChallengeSami Al Hajjar, Ziad A. Memish, Kenneth McIntosh — 2013
• Identification and functions of usefully disordered proteins.A. Keith Dunker, Celeste J. Brown, Zoran Obradović — 2002
• Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regionsGkikas Magiorkinis, Emmanouil Magiorkinis, Dimitrios Paraskevis — 2004
• Bat-to-human: spike features determining ‘host jump’ of coronaviruses SARS-CoV, MERS-CoV, and beyondGuangwen Lu, Qihui Wang, George F. Gao — 2015
• The membrane-anchored serine protease, TMPRSS2, activates PAR-2 in prostate cancer cells.Susan K. Wilson, Brett Greer, John D. Hooper — 2005
• Catalytic cleavage of the androgen-regulated TMPRSS2 protease results in its secretion by prostate and prostate cancer epithelia.Daniel Afar, Igor Vivanco, René Hubert — 2001
• Fuzzy complexes: Specific binding without complete foldingRashmi Sharma, Zsolt Ráduly, Márton Miskei — 2015
• Length-dependent prediction of protein intrinsic disorderKang Peng, Predrag Radivojac, Slobodan Vučetić — 2006
• Type II transmembrane serine proteases.Qingyu Wu — 2003
• Identification of the Receptor-Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1Zhaohui Qian, Xiuyuan Ou, Luiz Gustavo Bentim Góes — 2015
• The multifaceted roles of intrinsic disorder in protein complexesVladimir N. Uversky — 2015
• Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes.Vladimir N. Uversky — 2011
• Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entryHeike Hofmann, Krzysztof Pyrć, Lia van der Hoek — 2005

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• Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in ChinaAiping Wu, Yousong Peng, Baoying Huang — 2020
• Deep convolutional neural networks for predicting leukemia-related transcription factor binding sites from DNA sequence dataJian He, Xuemei Pu, Menglong Li — 2020
• Coronavirus: Scientometrics of 50 Years of Global Scientific ProductionsFarshid Danesh, Somayeh Ghavidel — 2020
• SARS-CoV-2/COVID-19 and Advances in Developing Potential Therapeutics and Vaccines to Counter this Emerging Pandemic Virus – A ReviewAli A. Rabaan, Shamsah H. Al-Ahmed, Ranjit Sah — 2020
• The genetic sequence, origin, and diagnosis of SARS-CoV-2Huihui Wang, Xuemei Li, Tao Li — 2020
• COVIDier: A Deep-learning Tool For Coronaviruses Genome And Virulence Proteins ClassificationPeter T. Habib, Alsamman M. Alsamman, Maha Saber-Ayad — 2020
• Kinetics of SARS-CoV-2 specific IgM and IgG responses in COVID-19 patientsBaoqing Sun, Ying Feng, Xiaoneng Mo — 2020
• SARS-CoV, MERS-CoV and SARS-CoV-2 infections in pregnancy and fetal developmentGuilherme Antonio de Souza Silva, Suéllen Pedrosa da Silva, Marcos Aurélio Santos da Costa — 2020
• Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target EngagementMathew A. Coban, Juliet Morrison, Sushila Maharjan — 2020
• Role of inflammatory markers in corona virus disease (COVID-19) patients: A reviewJyoti Upadhyay, Nidhi Tiwari, Mohd Nazam Ansari — 2020
• An Introduction to SARS Coronavirus 2; Comparative Analysis with MERS and SARS Coronaviruses: A Brief ReviewMahsa Taherizadeh, Alireza Tabibzadeh, Mahshid Panahi — 2020
• Current Understanding, Knowledge Gaps and a Perspective on the Future of COVID-19 Infections: A Systematic ReviewAnita Chakravarti, Shalini Upadhyay, Tanisha Bharara — 2020
• Molecular diagnosis of COVID-19: Current situation and trend in China (Review)Ning Li, Pengtao Wang, Xinyue Wang — 2020
• Genetic and pathogenic characterization of SARS-CoV-2: a reviewAfsane Bahrami, Gordon A. Ferns — 2020
• The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humansKatarzyna Pancer, Aleksandra Milewska, Katarzyna Owczarek — 2020
• SARS-CoV-2/COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemicAli A. Rabaan, Shamsah H. Al-Ahmed, Ranjit Sah — 2020
• The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategiesElahe Seyed Hosseini, Narjes Riahi Kashani, Hossein Nikzad — 2020
• Insights into the Origin, Transmission and Outbreak of Coronavirus Disease (Covid 19): A Recent StudyJhilam Majumder, Subhadeep Das, Shubhasis Dan — 2020
• Coronavirus and Its effect on the respiratory system: Is there any association between pneumonia and immune cellsBesharat Rahimi, Ahmad Vesal, Maryam Edalatifard — 2020
• Emergence of Avian coronavirus genotype GI-11 in ColombiaNelson Fernando Santana-Clavijo, Paulo Eduardo Brandão — 2020

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