Software tools for Biological discovery.
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HIVtoolbox2
The goal of this project is to create an integrated webtool that can be used to investigate potential drug targets in HIV. HIVtoolbox2 is an analytic tool that integrates data for all HIV proteins. The application has a sequence window that maps domains, functional sites, protein-protein interactions, and potential functional minimotifs to the sequence (Sargeant et al., 2014 pending, (Sargeant et al, 2008). The sequence is coupled to six interactive structure viewers that are synchronized. These structure windows show structures colored by domains, predicted minimotifs, functional sites, protein-protein interactions, sequence conservation, drug resistance mutations, drug binding sites, and immune eptipopes. Sequence conservation is calculated for many thousand different sequences from isolates. This is integrated with a species/group/clade selected and sequence alignment/PSSM display. HIVtoolbox was built by David Sargeant, Sandeep Deverasetty, Angel Villahoz Baleta, and Mike Hedden. Relevant links: Wikipedia article; IAS 2012 meeting presentation; HIVToolbox2 user guide; HIVToolbox2 video tutorials. The original version of HIVToolbox v1.0, a HIVToolbox v1.0 User Guide, and HIVToolbox v1.0 Video tutorials are still available, but no longer maintained.

PLEASE CITE USE OF HIVTOOLBOX WITH THIS PAPER:
David P. Sargeant, et al. (2014) The HIVToobox 2 web system integrates sequence, structure, function and mutation analysis. PLoS One, 9, e98810. PMID: 24886930

Sargeant D, Deverasetty S, Luo Y, Baleta AV, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, and Schiller MR (2011) HIVToolbox, an integrated web application for investigating HIV. PLoS One, 6, e20122. PMID: 21647445