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An Algorithm for Describing the Convex and Concave Shape of Protein Surface

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Data Science (ICPCSEE 2018)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 902))

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Abstract

Protein surface plays a key role in many biological processes. Most proteins participate in the life activities of cells via binding to other proteins or ligand molecules. It is an important work to study protein structure and function by analyzing the protein surface shape. Based on the CX algorithm and the 2D fngerprint-base method, we proposed a FCX method to identify the morphology of bulges and depressions on the protein surface. The experimental results show that the FCX algorithm has a more desirable outcome than CX algorithm. The FCX algorithm has a higher correlation with the convex and concave features than CX values with solvent accessibility, solvent accessibility, and B-factor’s Pearson correlation coefficient. This result shows that the FCX algorithm can describe the shape of the protein surface residues more accurately than the CX algorithm.

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Acknowledgements

This work was supported by Natural Science Foundation of Henan province (182300410368,182300410130,182300410306), the Production and Learning Cooperation and Cooperative Education Project of Ministry of Education of China (201702115008), National Natural Science Foundation of China (No. 61772176, 61402153), the Science and Technology Research Key Project of Educational Department of Henan Province (No. 16A520016, 17B520002, 17B520036), Key Project of Science and Technology Department of Henan Province (No. 1821022 10208, 142102210056, 17B520002), Ph.D. Research Startup Foundation of Henan Normal University (Nos. qd15130, qd15132, qd15129), China Postdoctoral Science Foundation (No. 2016M602247), the Young Scholar Program of Henan Province (2017GGJS041), and the Key Scientific and Technological Project of Xinxiang City Of China (No. CXGG17002).

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Authors and Affiliations

  1. Department of Computer Science and Technology, College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, Henan Province, China

    Wei Wang, Keliang Li, Hehe Lv, Lin Sun, Shiguang Zhang, Yun Zhou, Yuan Zhao & Jingjing Xv

  2. Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Xinxiang, 453007, Henan Province, China

    Wei Wang

  3. School of Aviation Engineering, Anyang University, Anyang, 455000, Henan Province, China

    Hongjun Zhang

  4. School of International Education, Xuchang University, Xuchang, 461000, Henan Province, China

    Jinling Shi

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  1. Wei Wang
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  2. Keliang Li
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  3. Hehe Lv
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  4. Lin Sun
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  5. Hongjun Zhang
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  6. Jinling Shi
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  7. Shiguang Zhang
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  8. Yun Zhou
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  9. Yuan Zhao
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  10. Jingjing Xv
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Corresponding author

Correspondence to Wei Wang .

Editor information

Editors and Affiliations

  1. Zhengzhou University, Zhengzhou, Henan, China

    Qinglei Zhou

  2. Xidian University, Xi’an, Shaanxi, China

    Qiguang Miao

  3. Harbin Institute of Technology, Harbin, China

    Hongzhi Wang

  4. Harbin University of Science and Technology, Harbin, China

    Wei Xie

  5. Zhengzhou Institute of Technology, Zhengzhou, China

    Yan Wang

  6. National Academy of Guo Ding Institute of Data Science, Beijing, China

    Zeguang Lu

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Wang, W. et al. (2018). An Algorithm for Describing the Convex and Concave Shape of Protein Surface. In: Zhou, Q., Miao, Q., Wang, H., Xie, W., Wang, Y., Lu, Z. (eds) Data Science. ICPCSEE 2018. Communications in Computer and Information Science, vol 902. Springer, Singapore. https://doi.org/10.1007/978-981-13-2206-8_3

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  • DOI: https://doi.org/10.1007/978-981-13-2206-8_3

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-13-2205-1

  • Online ISBN: 978-981-13-2206-8

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