Exhaustive enumeration of fragment-assembled protein conformations

초록

In a fragment assembly method of protein structure prediction, fragments of the local structure of a protein are collected from a structural database, and the combination that minimizes the free-energy function is considered as the model for the global structure. In contrast to pure physics-based methods where all dihedral angles are allowed to vary continuously, the conformational space is reduced to a finite, discrete set. However, only stochastic global optimization methods have been used for the conformational search in the past, and there has been no attempt to enumerate conformations generated by fragment assembly. In this work, we perform an exhaustive enumeration of protein conformations generated by fragment assembly for two small proteins, 112y and 1e01, that belong to distinct structural classes, and perform various analyses.

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