Scholarlink

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.

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field

  • 实验方案

  • 发表日期：

    2025年

查看全文
  • Emilia A. Lubecka,
  • Cezary Czaplewski,
  • Adam K. Sieradzan,
  • Agnieszka G. Lipska,
  • Łukasz Dziadek,
  • Adam Liwo

摘要

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.