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Open Access Green as soon as Postprint is submitted to ZB.
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes.
J. Comput. Chem. 43, 1633-1640 (2022)
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.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Explicit Solvent ; Glycosaminoglycan Modeling ; Molecular Docking ; Molecular Dynamics ; Repulsive Scaling Replica Exchange
ISSN (print) / ISBN
0192-8651
e-ISSN
1096-987X
Quellenangaben
Volume: 43,
Issue: 24,
Pages: 1633-1640
Publisher
Wiley
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Structural Biology (STB)
Grants
Narodowe Centrum Nauki