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Graphics Native Approach to Identifying Surface Atoms of Macromolecules

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GPU Computing and Applications

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Abstract

Classification of “surface atoms” or “interior atoms” of proteins or other macromolecules is significant for many biochemical tasks, particularly for molecular docking. We present a simple and easy-to-implement algorithm for identifying surface atoms of macromolecules from interior atoms. Unlike existing methods that are based on geometry computations, our approach takes the advantage of graphics hardware, and most of the computations are fulfilled with graphics processing unit (GPU). The algorithm can be easily incorporated within visualization applications for macromolecules to enable the removal of interior atoms from a macromolecular structure, thus simplifying the graphics display and manipulation.

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Acknowledgments

The authors would like to thank the partial funding support from Singapore MOE Tier 1 (RG 10/12).

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Authors and Affiliations

  1. State Key Lab of CAD&CG, Zhejiang University, Hangzhou, China, 310027

    Huagen Wan

  2. Institute for Media Innovation, Nanyang Technological University, Singapore, Singapore, 637553

    Yunqing Guan

  3. School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore, 639798

    Yiyu Cai

Authors
  1. Huagen Wan
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  2. Yunqing Guan
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  3. Yiyu Cai
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Correspondence to Yiyu Cai .

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Editors and Affiliations

  1. Nanyang Technological University, Singapore, Singapore

    Yiyu Cai

  2. Nvidia, Singapore, Singapore

    Simon See

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Wan, H., Guan, Y., Cai, Y. (2015). Graphics Native Approach to Identifying Surface Atoms of Macromolecules. In: Cai, Y., See, S. (eds) GPU Computing and Applications. Springer, Singapore. https://doi.org/10.1007/978-981-287-134-3_6

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  • DOI: https://doi.org/10.1007/978-981-287-134-3_6

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-287-133-6

  • Online ISBN: 978-981-287-134-3

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