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.
Authors
- dr hab. inż. Emilia Lubecka link open in new tab ,
- Dr hab. Cezary Czaplewski,
- dr Adam Sieradzan,
- dr inż. Agnieszka Lipska link open in new tab ,
- Lukasz Dziadek,
- Adam Liwo
Additional information
- DOI
- Digital Object Identifier link open in new tab 10.1007/978-1-0716-4196-5_2
- Category
- Publikacja monograficzna
- Type
- rozdział, artykuł w książce - dziele zbiorowym /podręczniku w języku o zasięgu międzynarodowym
- Language
- angielski
- Publication year
- 2025
