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PROCEDIA
2011

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases

8 years 1 months ago
GPU-accelerated Chemical Similarity Assessment for Large Scale Databases
The assessment of chemical similarity between molecules is a basic operation in chemoinformatics, a computational area concerning with the manipulation of chemical structural information. Comparing molecules is the basis for a wide range of applications such as searching in chemical databases, training prediction models for virtual screening or aggregating clusters of similar compounds. However, currently available multimillion databases represent a challenge for conventional chemoinformatics algorithms raising the necessity for faster similarity methods. In this paper, we extensively analyze the advantages of using many-core architectures for calculating some commonly-used chemical similarity coefficients such as Tanimoto, Dice or Cosine. Our aim is to provide a wide-breath proof-of-concept regarding the usefulness of GPU architectures to chemoinformatics, a class of computing problems still uncovered. In our work, we present a general GPU algorithm for all-to-all chemical comparison...
Marco Maggioni, Marco D. Santambrogio, Jie Liang
Added 17 Sep 2011
Updated 17 Sep 2011
Type Journal
Year 2011
Where PROCEDIA
Authors Marco Maggioni, Marco D. Santambrogio, Jie Liang
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