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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
Abstract
Glycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes of biomolecules. Therefore, there is a lack of modeling tools designed specifically for docking GAGs. One has to rely on existing docking software developed mostly for small drug molecules substantially differing from GAGs in their basic physico-chemical properties. In this study, we present an updated protocol for docking GAGs based on the Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) that includes explicit solvent description. The use of this water model improved docking performance both in terms of its accuracy and speed. This method represents a significant computational progress in GAG-related research.
Citations
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Authors (6)
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Mateusz Marcisz
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Margrethe Gaardløs
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Till Siebenmorgen
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Martin Zachariasen
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Sergey A. Samsonov
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Details
- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
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JOURNAL OF COMPUTATIONAL CHEMISTRY
no. 43,
pages 1633 - 1640,
ISSN: 0192-8651 - Language:
- English
- Publication year:
- 2022
- Bibliographic description:
- Marcisz M., Gaardløs M., Bojarski K., Siebenmorgen T., Zachariasen M., Samsonov S. A.: Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes// JOURNAL OF COMPUTATIONAL CHEMISTRY -Vol. 43,iss. 24 (2022), s.1633-1640
- DOI:
- Digital Object Identifier (open in new tab) 10.1002/jcc.26965
- Sources of funding:
-
- COST_FREE
- Verified by:
- Gdańsk University of Technology
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