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Article

Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Filip Jagodzinski and Kevin Molloy
Molecules 2021, 26(8), 2329; https://doi.org/10.3390/molecules26082329
Received: 16 March 2021 / Revised: 12 April 2021 / Accepted: 13 April 2021 / Published: 16 April 2021
To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence. View Full-Text
Keywords: protein conformations; conformational pathways; rapidly exploring random trees algorithm; rigidity analysis protein conformations; conformational pathways; rapidly exploring random trees algorithm; rigidity analysis
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MDPI and ACS Style

Afrasiabi, F.; Dehghanpoor, R.; Haspel, N. Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC. Molecules 2021, 26, 2329. https://doi.org/10.3390/molecules26082329

AMA Style

Afrasiabi F, Dehghanpoor R, Haspel N. Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC. Molecules. 2021; 26(8):2329. https://doi.org/10.3390/molecules26082329

Chicago/Turabian Style

Afrasiabi, Fatemeh, Ramin Dehghanpoor, and Nurit Haspel. 2021. "Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC" Molecules 26, no. 8: 2329. https://doi.org/10.3390/molecules26082329

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