The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.
There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4041786?pdf=render |
| _version_ | 1818020082393022464 |
|---|---|
| author | David P Sargeant Sandeep Deverasetty Christy L Strong Izua J Alaniz Alexandria Bartlett Nicholas R Brandon Steven B Brooks Frederick A Brown Flaviona Bufi Monika Chakarova Roxanne P David Karlyn M Dobritch Horacio P Guerra Michael W Hedden Rma Kumra Kelvy S Levitt Kiran R Mathew Ray Matti Dorothea Q Maza Sabyasachy Mistry Nemanja Novakovic Austin Pomerantz Josue Portillo Timothy F Rafalski Viraj R Rathnayake Noura Rezapour Sarah Songao Sean L Tuggle Sandy Yousif David I Dorsky Martin R Schiller |
| author_facet | David P Sargeant Sandeep Deverasetty Christy L Strong Izua J Alaniz Alexandria Bartlett Nicholas R Brandon Steven B Brooks Frederick A Brown Flaviona Bufi Monika Chakarova Roxanne P David Karlyn M Dobritch Horacio P Guerra Michael W Hedden Rma Kumra Kelvy S Levitt Kiran R Mathew Ray Matti Dorothea Q Maza Sabyasachy Mistry Nemanja Novakovic Austin Pomerantz Josue Portillo Timothy F Rafalski Viraj R Rathnayake Noura Rezapour Sarah Songao Sean L Tuggle Sandy Yousif David I Dorsky Martin R Schiller |
| author_sort | David P Sargeant |
| collection | DOAJ |
| description | There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com]. |
| first_indexed | 2024-04-14T08:01:19Z |
| format | Article |
| id | doaj.art-50992c4abf2f4d018d2567fbf1d4b035 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-14T08:01:19Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-50992c4abf2f4d018d2567fbf1d4b0352022-12-22T02:04:54ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0196e9881010.1371/journal.pone.0098810The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.David P SargeantSandeep DeverasettyChristy L StrongIzua J AlanizAlexandria BartlettNicholas R BrandonSteven B BrooksFrederick A BrownFlaviona BufiMonika ChakarovaRoxanne P DavidKarlyn M DobritchHoracio P GuerraMichael W HeddenRma KumraKelvy S LevittKiran R MathewRay MattiDorothea Q MazaSabyasachy MistryNemanja NovakovicAustin PomerantzJosue PortilloTimothy F RafalskiViraj R RathnayakeNoura RezapourSarah SongaoSean L TuggleSandy YousifDavid I DorskyMartin R SchillerThere is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com].http://europepmc.org/articles/PMC4041786?pdf=render |
| spellingShingle | David P Sargeant Sandeep Deverasetty Christy L Strong Izua J Alaniz Alexandria Bartlett Nicholas R Brandon Steven B Brooks Frederick A Brown Flaviona Bufi Monika Chakarova Roxanne P David Karlyn M Dobritch Horacio P Guerra Michael W Hedden Rma Kumra Kelvy S Levitt Kiran R Mathew Ray Matti Dorothea Q Maza Sabyasachy Mistry Nemanja Novakovic Austin Pomerantz Josue Portillo Timothy F Rafalski Viraj R Rathnayake Noura Rezapour Sarah Songao Sean L Tuggle Sandy Yousif David I Dorsky Martin R Schiller The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PLoS ONE |
| title | The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. |
| title_full | The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. |
| title_fullStr | The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. |
| title_full_unstemmed | The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. |
| title_short | The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. |
| title_sort | hivtoolbox 2 web system integrates sequence structure function and mutation analysis |
| url | http://europepmc.org/articles/PMC4041786?pdf=render |
| work_keys_str_mv | AT davidpsargeant thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sandeepdeverasetty thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT christylstrong thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT izuajalaniz thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT alexandriabartlett thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nicholasrbrandon thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT stevenbbrooks thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT frederickabrown thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT flavionabufi thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT monikachakarova thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT roxannepdavid thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT karlynmdobritch thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT horaciopguerra thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT michaelwhedden thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT rmakumra thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT kelvyslevitt thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT kiranrmathew thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT raymatti thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT dorotheaqmaza thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sabyasachymistry thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nemanjanovakovic thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT austinpomerantz thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT josueportillo thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT timothyfrafalski thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT virajrrathnayake thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nourarezapour thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sarahsongao thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT seanltuggle thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sandyyousif thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT davididorsky thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT martinrschiller thehivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT davidpsargeant hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sandeepdeverasetty hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT christylstrong hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT izuajalaniz hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT alexandriabartlett hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nicholasrbrandon hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT stevenbbrooks hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT frederickabrown hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT flavionabufi hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT monikachakarova hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT roxannepdavid hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT karlynmdobritch hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT horaciopguerra hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT michaelwhedden hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT rmakumra hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT kelvyslevitt hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT kiranrmathew hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT raymatti hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT dorotheaqmaza hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sabyasachymistry hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nemanjanovakovic hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT austinpomerantz hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT josueportillo hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT timothyfrafalski hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT virajrrathnayake hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT nourarezapour hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sarahsongao hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT seanltuggle hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT sandyyousif hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT davididorsky hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis AT martinrschiller hivtoolbox2websystemintegratessequencestructurefunctionandmutationanalysis |