HIVToolbox: Difference between revisions
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{{technical|date=November 2011}} |
{{technical|date=November 2011}} |
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HIV is the <u>virus</u> that causes the <u>disease</u> AIDS. |
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'''HIVToolbox''' is an internet application that helps scientists identify and develop new hypotheses as well as facilitate interpretation of experiments, with the goal of helping scientist better understand [[HIV]] and to identify new potential drug targets in HIV.<ref> |
'''HIVToolbox''' is an internet application that helps scientists identify and develop new hypotheses as well as facilitate interpretation of experiments, with the goal of helping scientist better understand [[HIV]] and to identify new potential drug targets in HIV.<ref> |
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{{Cite journal |
{{Cite journal |
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|title= HIVToolbox, an integrated web application for investigating HIV |
|title= HIVToolbox, an integrated web application for investigating HIV |
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|journal=PLoS ONE |volume=6 |pages= e20122 |year=2011 |pmid=21647445 |pmc= 310207 |doi= 10.1371/journal.pone.0020122}}</ref> |
|journal=PLoS ONE |volume=6 |pages= e20122 |year=2011 |pmid=21647445 |pmc= 310207 |doi= 10.1371/journal.pone.0020122}}</ref> |
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<blockquote>''In plain English:''</blockquote> |
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<blockquote>The above is saying that a bunch of nerdy scientists have created a computer gizmo from some programming language to help out people with AIDS (HIV is the <u>virus</u> that causes the <u>disease</u> AIDS, by the way, so HIV/AIDS are sort of the same thing here).</blockquote> |
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<blockquote>HIV sucks. Instead of being "Strep throat" or "Strep", which can be remedied by half a dozen drugs that ''kill'' the bacteria, we have no drugs that can actually kill HIV so far, and scientists are puzzled, because it's such a hard disease to treat. The one thing they know is that if they make this "case file" with all of the virus's fingerprints, etc., and team up online, eventually someone somewhere will figure this all out and fix AIDS someday. But right now this is just a computer program to display all the data. So far, no cure. Just technology.</blockquote> |
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HIV, like other viruses has a relatively small [[genome]], and uses minimotifs encoded in its proteins to help manipulate host proteins to facilitate its reproduction.<ref> |
HIV, like other viruses has a relatively small [[genome]], and uses minimotifs encoded in its proteins to help manipulate host proteins to facilitate its reproduction.<ref> |
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{{Cite journal |
{{Cite journal |
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<!-- we don't need a |
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|last1=Kadaveru |first1=Krishna |
|last1=Kadaveru |first1=Krishna |
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|last2=Vyas |first2=Jay |
|last2=Vyas |first2=Jay |
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}}</ref> The database also contains calculated amino acid conservation for all HIV proteins based on known isolates sequences and also segregated by viral clades and subtypes. These data can be observed in a [[position-specific scoring matrix]]. |
}}</ref> The database also contains calculated amino acid conservation for all HIV proteins based on known isolates sequences and also segregated by viral clades and subtypes. These data can be observed in a [[position-specific scoring matrix]]. |
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<blockquote>''In plain English:''</blockquote> |
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<blockquote>They can't figure out how exactly to stop it, or even exactly how it attaches to cells to make people sick. But they say "hey, it could be worse, right?" and are trying to be optimistic. So they're taking everything they know about this pesky virus and putting it all in a computerized database where they can look at it again and again from different angles. Hopefully, someday a scientist will find a cure and maybe, they're saying, the scientist will be helped by using this tool they gave them. Right now, no cure yet. Just chatter about how to get going.</blockquote> |
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<!-- editor note: Tacky, but better than jargon. Please, improve this article if you can! --> |
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==References== |
==References== |
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Revision as of 17:29, 10 April 2014
 | This article may be too technical for most readers to understand. (November 2011) |
HIV is the virus that causes the disease AIDS. HIVToolbox is an internet application that helps scientists identify and develop new hypotheses as well as facilitate interpretation of experiments, with the goal of helping scientist better understand HIV and to identify new potential drug targets in HIV.[1]
HIV, like other viruses has a relatively small genome, and uses minimotifs encoded in its proteins to help manipulate host proteins to facilitate its reproduction.[2] HIVtoolbox is an internet application that runs off of a MySQL database designed to integrate HIV data for protein sequences derived from many different isolates, protein structures, protein domains, protein-protein interactions, functional elements in proteins, and known and predicted minimotifs from the Minimotif Miner database.[3][4] The database also contains calculated amino acid conservation for all HIV proteins based on known isolates sequences and also segregated by viral clades and subtypes. These data can be observed in a position-specific scoring matrix.
References
- ^
Sargeant, David; Deverasetty, Sandeep; Luo, Yang; Baleta, Angel V.; Zobrist, Stephanie R.; Rathnayake, Viraj; Tusso, Jacqueline C.; Vyas, Jay; Muesing, Mark A.; Schiller, Martin R. (2011). "HIVToolbox, an integrated web application for investigating HIV". PLoS ONE. 6: e20122. doi:10.1371/journal.pone.0020122. PMC 310207. PMID 21647445.
{{cite journal}}: Unknown parameter|displayauthors=ignored (|display-authors=suggested) (help)CS1 maint: unflagged free DOI (link) - ^ Kadaveru, Krishna; Vyas, Jay; Schiller, Martin R. (2008). "Viral infection and human disease - insights from minimotifs". Frontiers in Bioscience. 13: 6455–71. PMC 2628544. PMID 18508672.
- ^
Rajasekaran, Sanguthevar; Balla, Sudha; Gradie, Patrick; Gryk, Michael R.; Kadaveru, Krishna; Kundeti, Vamsi; MacIejewski, Mark W.; Mi, Tian; Rubino, Nicholas (2009). "Minimotif miner 2nd release: a database and web system for motif search". Nucleic Acids Research. 37 (Database issue): D185–90. doi:10.1093/nar/gkn865. PMC 2686579. PMID 18978024.
{{cite journal}}: Unknown parameter|displayauthors=ignored (|display-authors=suggested) (help) - ^
Balla, Sudha; Thapar, Vishal; Verma, Snigda; Luong, ThaiBinh; Faghri, Tanaz; Huang, Chun-Hsi; Rajasekaran, Sanguthevar; del Campo, Jacob J; Shinn, Jessica H; Mohler, William A; Maciejewski, Mark W; Gryk, Michael R; Piccirillo, Bryan; Schiller, Stanley R; Schiller, Martin R (2006). "Minimotif Miner, a tool for investigating protein function". Nature Methods. 3: 175–177. doi:10.1038/nmeth856. PMID 16489333.
{{cite journal}}: Unknown parameter|displayauthors=ignored (|display-authors=suggested) (help)