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A kernel for open source drug discovery in tropical diseases.

Publication ,  Journal Article
Ortí, L; Carbajo, RJ; Pieper, U; Eswar, N; Maurer, SM; Rai, AK; Taylor, G; Todd, MH; Pineda-Lucena, A; Sali, A; Marti-Renom, MA
Published in: PLoS neglected tropical diseases
January 2009

Conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private-public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues-open source drug discovery-has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such "kernels".HERE, WE USE A COMPUTATIONAL PIPELINE FOR: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other.The TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases.

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Published In

PLoS neglected tropical diseases

DOI

EISSN

1935-2735

ISSN

1935-2727

Publication Date

January 2009

Volume

3

Issue

4

Start / End Page

e418

Related Subject Headings

  • Tropical Medicine
  • Tropical Medicine
  • Software
  • Models, Molecular
  • Humans
  • Drug Discovery
  • Computer Simulation
  • Antiparasitic Agents
  • 42 Health sciences
  • 32 Biomedical and clinical sciences
 

Citation

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Ortí, L., Carbajo, R. J., Pieper, U., Eswar, N., Maurer, S. M., Rai, A. K., … Marti-Renom, M. A. (2009). A kernel for open source drug discovery in tropical diseases. PLoS Neglected Tropical Diseases, 3(4), e418. https://doi.org/10.1371/journal.pntd.0000418
Ortí, Leticia, Rodrigo J. Carbajo, Ursula Pieper, Narayanan Eswar, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, et al. “A kernel for open source drug discovery in tropical diseases.PLoS Neglected Tropical Diseases 3, no. 4 (January 2009): e418. https://doi.org/10.1371/journal.pntd.0000418.
Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, et al. A kernel for open source drug discovery in tropical diseases. PLoS neglected tropical diseases. 2009 Jan;3(4):e418.
Ortí, Leticia, et al. “A kernel for open source drug discovery in tropical diseases.PLoS Neglected Tropical Diseases, vol. 3, no. 4, Jan. 2009, p. e418. Epmc, doi:10.1371/journal.pntd.0000418.
Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for open source drug discovery in tropical diseases. PLoS neglected tropical diseases. 2009 Jan;3(4):e418.

Published In

PLoS neglected tropical diseases

DOI

EISSN

1935-2735

ISSN

1935-2727

Publication Date

January 2009

Volume

3

Issue

4

Start / End Page

e418

Related Subject Headings

  • Tropical Medicine
  • Tropical Medicine
  • Software
  • Models, Molecular
  • Humans
  • Drug Discovery
  • Computer Simulation
  • Antiparasitic Agents
  • 42 Health sciences
  • 32 Biomedical and clinical sciences