ArticleJournal of computational biology : a journal of computational molecular cell biology2016
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- OSPREY 3.0: Open-source protein redesign for you, with powerful new features.Journal of computational chemistry · 2018Article
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7 authors.
Funding
Abstract
Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches.
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Registered trials
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