Open Access

ARTICLE

Robust Reduction Method for Biomolecules Modeling

Kilho Eom¹, Jeong-Hee Ahn², Seung-Chul Baek², Jae-In Kim², Sungsoo Na^2,3

1 Nano-Bio Research Center, Korea Institute of Science &Technology, Hawolgok-dong, Seongbuk-gu, Seoul, 136-791, Korea (e-mail: eomkh@kist.re.kr).
2 Department of Mechanical Enginrrering , Korea University, Anam-dong, Sungbuk-gu, Seoul, 136-713, Korea (e-mails: {shibuya, takeoff2, jay414, nass} @korea.ac.kr).
3 Corresponding author.

Computers, Materials & Continua 2007, 6(1), 35-42. https://doi.org/10.3970/cmc.2007.006.035

Abstract

This paper concerns the application and demonstration of robust reduction methodology for biomolecular structure modeling, which is able to estimate dynamics of large proteins. The understanding of large protein dynamics is germane to gain insight into biological functions related to conformation change that is well described by normal modes. In general, proteins exhibit the complicated potential field and the large degrees of freedom, resulting in the computational prohibition for large protein dynamics. In this article, large protein dynamics is investigated with modeling reduction schemes. The performance of hierarchical condensation methods implemented in the paper is compared with that obtained from full original model, successfully demonstrating robustness of reduction method. The examples presented in these results also show that the computational accuracy of reduction method is maintained, while computational cost is reduced.

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Keywords

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