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Virus CKB 2.0: Viral-associated disease-specific chemogenomics knowledgebase

Hao, Yixuan (2022) Virus CKB 2.0: Viral-associated disease-specific chemogenomics knowledgebase. Master's Thesis, University of Pittsburgh. (Unpublished)

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Given that mutations in viruses always occur during evolution, the doctor calls for a flu vaccine every year. Vaccines obtained from diseased strains have a protective effect of 40%-60%. However, if the diseased strain is mutated, the vaccine will lose its effect. Therefore, it is very necessary to track the data and structure of different viruses for research purposes. Viruses have different domains that are related to the invasion or replication of the virus, so drugs targeting these different domains can provide therapeutic potential for the treatment of diseases caused by these viruses. To facilitate the research of viral infection disease, we updated our Virus-CKB 1.0 to 2.0 by adding structure information of another ten viruses and integrating new functions (e.g., protein-protein docking). To date, Virus-CKB 2.0 archived 65 antiviral drugs in the market, 178 viral-related targets with 291 available 3D crystal or cryo-EM structures, and 3766 chemical agents reported for these target proteins. Moreover, Virus-CKB 2.0 is implemented with web applications for the prediction of the relevant protein targets and analysis and visualization of the outputs, including Molecular Complex Characterizing System (MCCS) protocol, HTDocking, TargetHunter, blood-brain barrier (BBB) predictor, Spider Plot, Protein-Protein docking, etc. The Virus-CKB 2.0 server is accessible at By using the established chemogenomics tools and algorithms and newly developed tools, we can screen FDA-approved drugs and chemical compounds that may bind to these proteins involved in viral-associated diseases regulation. If the virus strain is mutated and the vaccine loses its effect, we can also screen out drugs that can be used to treat the mutated virus in a short time. For some FDA-approved drugs, we can also perform drug repurposing through Virus-CKB 2.0.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Hao, Yixuanyih83@pitt.eduyih83
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairWang,
Committee MemberLevent, KirisciLevent@pitt.edulevent
Committee MemberXie, XiangqunSean.Xie@pitt.eduSean.Xie
Thesis AdvisorFeng, Zhiweizhf11@pitt.eduzhif11
Date: 6 April 2022
Date Type: Publication
Defense Date: 30 March 2022
Approval Date: 6 April 2022
Submission Date: 4 April 2022
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 73
Institution: University of Pittsburgh
Schools and Programs: School of Pharmacy > Pharmaceutical Sciences
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: virus knowledgebase, dengue virus, online drug discovery, drug repurposing
Date Deposited: 06 Apr 2022 13:46
Last Modified: 06 Apr 2022 13:46


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