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• W2048563428 abstract "Methods for protein structure (3D)–sequence (1D) compatibility evaluation (threading) have been developed during the past decade. The protocol in which a sequence can recognize its compatible structure in the structural library (i.e., the fold recognition or the forward-folding search) is available for the structure prediction of new proteins. However, the reverse protocol, in which a structure recognizes its homologous sequences among a sequence database, named the inverse-folding search, is a more difficult application. In this study, we have investigated the feasibility of the latter approach. A structural library, composed of about 400 well-resolved structures with mutually dissimilar sequences, was prepared, and 163 of them had remote homologs in the library. We examined whether they could correctly seek their homologs by both forward-and inverse-folding searches. The results showed that the inverse-folding protocol is more effective than the forward-folding protocol, once the reference states of the compatibility functions are appropriately adjusted. This adjustment only slightly affects the ability of the forward-folding search. We noticed that the scoring, in which a given sequence is re-mounted onto a structure according to the 3D–1D alignment determined by the dynamic programming method, is only effective in the forward-folding protocol and not in the inverse-folding protocol. Namely, the inverse-folding search works significantly better with the score given by the 3D–1D alignment per se, rather than that obtained by the re-mounting. The implications of these results are discussed." @default.
• W2048563428 created "2016-06-24" @default.
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• W2048563428 date "1999-01-01" @default.
• W2048563428 modified "2023-10-17" @default.
• W2048563428 title "Feasibility in the inverse protein folding protocol" @default.
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• W2048563428 doi "https://doi.org/10.1110/ps.8.5.1001" @default.
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