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A critical assessment of finite element modeling approach for protein dynamics

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Abstract

Finite element (FE) modeling approach has emerged as an efficient way of calculating the dynamic properties of supramolecular protein structures and their complexes. Its efficiency mainly stems from the fact that the complexity of three-dimensional shape of a molecular surface dominates the computational cost rather than the molecular size or the number of atoms. However, no critical evaluation of the method has been made yet particularly for its sensitivity to the parameters used in model construction. Here, we make a close investigation on the effect of FE model parameters by analyzing 135 representative protein structures whose normal modes calculated using all-atom normal mode analysis are publicly accessible online. Results demonstrate that it is more beneficial to use a contour surface of electron densities as the molecular surface, in general, rather than to employ a solvent excluded surface, and that the solution accuracy is almost insensitive to the model parameters unless we avoid extreme values leading to an inaccurate depiction of the characteristic shapes.

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Authors and Affiliations

  1. Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea

    Giseok Yun, Jaehoon Kim & Do-Nyun Kim

  2. Institute of Advanced Machines and Design, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea

    Do-Nyun Kim

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  1. Giseok Yun
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  2. Jaehoon Kim
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  3. Do-Nyun Kim
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Correspondence to Do-Nyun Kim.

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Funding

This research was supported by the EDucation-research Integration through Simulation On the Net (EDISON) Program (Grant No. 2014M3C1A6038842), the Global Frontier R&D Program on Center for Wave Energy Control based on Metamaterials (Grant No. 2014M3A6B3063711), and the Basic Science Research Program (Grant No. 2016R1C1B2011098) through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning.

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Yun, G., Kim, J. & Kim, DN. A critical assessment of finite element modeling approach for protein dynamics. J Comput Aided Mol Des 31, 609–624 (2017). https://doi.org/10.1007/s10822-017-0027-4

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  • DOI: https://doi.org/10.1007/s10822-017-0027-4

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