HIVToolbox

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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 scientists better understand HIV, the virus that causes AIDS, and to identify new potential drug targets.[1]

The information about HIV includes the different parts of the HIV proteins, often referred to as domains. Smaller regions of the proteins called minimotifs are also present in HIV proteins. These minimotifs, also called short linear motifs encode different molecular functions in HIV proteins.[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] Other amino acids involved in molecular functions such as catalysis, dimerization, etc. are also included. The database for the program also contains calculated amino acid conservation for all HIV proteins. This helps to identify regions of the virus that do not change, thus are thought to represent important regions. The 2nd release of HIVToolbox, HIVToolbox2 also contains information about the locations on the proteins where different HIV drugs bind, and their spatial relationship to the mutations that arise in HIV and render the virus resistant to the drug.

References[edit]

  1. ^ 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. 
  2. ^ Kadaveru, Krishna; Vyas, Jay; Schiller, Martin R. (2008). "Viral infection and human disease - insights from minimotifs". Frontiers in Bioscience 13: 6455–71. doi:10.2741/3166. PMC 2628544. PMID 18508672. 
  3. ^ 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. 
  4. ^ 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.