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- W2624494187 abstract "To calculate the tertiary structure of a protein from its amino acid se- quence, the thermodynamic approach requires a potential function of sequence and conforma- tion that has its global minimum at the native conformation for many different proteins. Here we study the behavior of such functions for the simplest model system that still has some of the features of the protein folding problem, namely two-dimensional square lattice chain configu- rations involving two residue types. First we show that even the given contact potential, which by definition is used to identify the fold- ing sequences and their unique native confor- mations, cannot always correctly select which sequences will fold to a given structure. Sec- ond, we demonstrate that the given contact po- tential is not always able to favor the native alignment of a native sequence on its own na- tive conformation over other gapped align- ments of different folding sequences onto that same conformation. Because of these shortcom- ings, even in this simple model system in which all conformations and all native sequences are known and determined directly by the given potential, we must reexamine our expectations for empirical potentials used for inverse folding and gapped alignment on more realistic repre- sentations of proteins. o 1996 Wiley-Liss, Ine." @default.
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- W2624494187 date "1996-10-01" @default.
- W2624494187 modified "2023-09-23" @default.
- W2624494187 title "Failures of Inverse Foldingand Threading with Gapped Alignment" @default.
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- W2624494187 doi "https://doi.org/10.11234/gi1990.7.278" @default.
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