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- W1995121095 abstract "It is believed that the atlas of existing protein structures is faithfully represented in the PDB. However, whether this atlas covers the full universe of possible protein structures is still a debated issue. By using a sophisticated numerical approach we performed an exhaustive exploration of the conformational space of a 60a.a. polypeptide chain described with an accurate all-atom potential. We generated ∼30,000 compact folds with at least 30% of secondary structure corresponding to local energy minima. This ensemble plausibly represents the universe of protein folds of similar length: indeed, all the known folds are represented with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. The new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the design of novel folds." @default.
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- W1995121095 date "2011-02-01" @default.
- W1995121095 modified "2023-09-25" @default.
- W1995121095 title "Exploring by Enhanced Sampling Techniques: The Protein’s Conformational Space Beyond the PDB" @default.
- W1995121095 doi "https://doi.org/10.1016/j.bpj.2010.12.1354" @default.
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