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Free energy approximations in simple lattice proteins

机译:简单晶格蛋白中的自由能近似

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This work addresses the question of whether it is possible to define simple pairwise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how reliable it could possibly be. In a two-dimensional, infinite Jattice model system one can calculate ex!lct free energies by exhaustive enumeration. A series of approximations were fitted to exact results to assess the feasibility and utility of pairwise free energy terms. Approximating the true free energy with pairwise interactions gives a poor fit with little transferability between systems of different size. Adding extra artificial terms to the approximation yields better fits, but does not impro.ve the ability to generalize from one system size to another. Furthermore, one cannot distinguish folding from nonfolding sequences via the approximated free energies. Most usefully, the methodology shows how one can assess the utility of various terms in lattice protein/polymer models.
机译:这项工作解决了是否有可能定义简单的成对相互作用项来近似蛋白质或聚合物的自由能的问题。与其问平均力潜力有多可靠,不如问它可能有多可靠。在二维无限Jattice模型系统中,可以通过穷举枚举计算出自由能。将一系列近似值拟合为精确结果,以评估成对自由能项的可行性和实用性。用成对的相互作用近似真实的自由能会导致拟合度很差,并且在不同大小的系统之间几乎没有可传递性。在近似中添加额外的人工项会产生更好的拟合,但不会提高从一个系统大小到另一个系统大小的泛化能力。此外,不能通过近似的自由能将折叠与非折叠序列区分开。最有用的方法是显示如何评估晶格蛋白质/聚合物模型中各种术语的效用。

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