Finding Cures for Tropical Diseases: Is Open Source an Answer?

Duke University, Durham, North Carolina, United States
PLoS Medicine (Impact Factor: 14.43). 01/2005; 1(3):e56. DOI: 10.1371/journal.pmed.0010056
Source: PubMed


The Tropical Disease Initiative will be a Web-based, community- wide effort where scientists from the public and private sectors join together to discover new treatments.

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Available from: Arti K Rai, Aug 20, 2014
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    • "feature allows community users to request modeling of additional complete genomes as our computational resources allow. This feature has been used, for example, to support the Tropical Disease Initiative ( (37–40) "
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    ABSTRACT: ModBase ( is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment ( ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server ( ModBase models are also available through the Protein Model Portal ( Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (, the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (, the FoXSDock server for protein-protein docking filtered by an SAXS profile (, the SAXS Merge server for automatic merging of SAXS profiles ( and the Pose & Rank server for scoring protein-ligand complexes ( In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.
    Nucleic Acids Research 11/2013; 42(Database issue). DOI:10.1093/nar/gkt1144 · 9.11 Impact Factor
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    • "The inputs of the broader community led to both changes in direction of the research and an acceleration of the science, leading to the publication in 2011 of a solution to the problem suitable for scale-up. While this was an important proof-of-concept, it begged the question of whether similar ideas could be applied to drug discovery, where the intellectual property landscape is more complicated, and the long-term funding regime less clear; such an idea had been mooted or started but a full campaign never tried (Maurer et al. 2004; Bradley et al. 2008). There have been major moves to make the drug discovery process more collaborative, such as via Product Development Partnerships like the Medicines for Malaria Venture (MMV) and the Drugs for Neglected Diseases Initiative (DNDi) or other ventures (Norman et al. 2011). "
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    ABSTRACT: SUMMARY Open science is a new concept for the practice of experimental laboratory-based research, such as drug discovery. The authors have recently gained experience in how to run such projects and here describe some straightforward steps others may wish to take towards more openness in their own research programmes. Existing and inexpensive online tools can solve many challenges, while some psychological barriers to the free sharing of all data and ideas are more substantial.
    Parasitology 08/2013; 141(1):1-10. DOI:10.1017/S0031182013001121 · 2.56 Impact Factor
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    • ", science [22] and medicine [23]. Why not apply what we have learned from the information technology revolution to nanotechnology as well? "
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    ABSTRACT: Despite being an extremely active area for patent applications, nanotechnology development is being impaired by current intellectual property law. In contrast to other emerging fields at their times, nanotechnology was born as the Bayh–Dole Act enabled universities to lock down fundamental research effectively preventing open competition. Both technical complexity and bureaucratic mishandling of nanotechnology patent applications have created a dense patent thicket of overlapping claims and rights. This intellectual property tragedy restricts downstream innovation by preventing development of more complex technologies due to exorbitant transaction costs. This article addresses this tragedy with the application of the free and open-source paradigm from software development as open-source methodologies will both accelerate nanotechnology innovation and improve the social return from public investment in nanotechnology research.
    Nano Today 08/2013; 8(4). DOI:10.1016/j.nantod.2013.04.001 · 15.00 Impact Factor
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