Exact enumeration of protein conformations from fragment assembly

초록

Efficient sampling of protein conformations is very important in computational studies of protein folding. The search space of the protein conformations can be reduced by utilizing bioinformatics. The frament assembly is one such method, where the local structures are selected from the fragment sets prepared using bioinformatics tool. The conformational space of proteins is reduced to a finite discrete set by using fragment assembly. The search space can be further reduced by introducing a consistency condition at the junction of the fragments. An algorithm for exact enuemration of such conformations are introduced, which can be used for generating cadidates of the native structure for a relatively short protein. © Published under licence by IOP Publishing Ltd.