Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk, Poland.
Phys Chem Chem Phys. 2011 Oct 14;13(38):16890-901. doi: 10.1039/c1cp20752k. Epub 2011 Jun 3.
We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described.
我们回顾了粗粒化的 UNited RESidue（UNRES）力场，该力场用于模拟蛋白质结构和动力学，这是我们实验室在过去几年中一直在开发的。UNRES 是一种基于物理的力场，其原型被定义为多肽链在水中的平均力势能，其中除了α-碳原子和侧链中心的坐标之外的所有自由度都已被积分掉。我们描述了 UNRES 的初始实现，该实现将蛋白质结构预测表述为对势能函数的全局最小值的搜索，以及随后的分子动力学和分子动力学实现的扩展，这使我们能够研究蛋白质折叠途径和热力学，以及将蛋白质结构预测问题重新表述为在折叠转变温度以下的温度下搜索具有最低自由能的构象系综。还描述了 UNRES 在研究生物学问题中的应用。
