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Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field
Abstract
Secondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental data, and the role of those in the modeling of protein structures, dynamics, and thermodynamics with the physics-based coarse-grained UNRES force field. Examples illustrating the methodology discussed and further directions of development are presented.
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Authors (6)
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Cezary Czaplewski Dr hab.
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Adam Sieradzan dr
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Lukasz Dziadek
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Adam Liwo
Cite as
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Keywords
Details
- Category:
- Monographic publication
- Type:
- rozdział, artykuł w książce - dziele zbiorowym /podręczniku w języku o zasięgu międzynarodowym
- Language:
- English
- Publication year:
- 2025
- Bibliographic description:
- Lubecka E., Czaplewski C., Sieradzan A., Lipska A., Dziadek L., Liwo A.: Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field// Prediction of Protein Secondary Structure/ : , 2025, s.19-41
- DOI:
- Digital Object Identifier (open in new tab) 10.1007/978-1-0716-4196-5_2
- Sources of funding:
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- Free publication
- Verified by:
- Gdańsk University of Technology
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