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Data from: Exploring the universe of protein structures beyond the Protein Data Bank

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Cossio P, Trovato A, Pietrucci F, Seno F, Maritan A, Laio A (2010) Exploring the universe of protein structures beyond the Protein Data Bank. PLoS Computational Biology 6(11): e1000957. doi:10.1371/journal.pcbi.1000957

Additionally, please cite the Dryad data package:

Cossio P, Trovato A, Pietrucci F, Seno F, Maritan A, Laio A (2010) Data from: Exploring the universe of protein structures beyond the Protein Data Bank. Dryad Digital Repository. doi:10.5061/dryad.1922
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Dryad Package Identifier doi:10.5061/dryad.1922    340 views  
Abstract It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least 30% of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set 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. Beside their conceptual relevance, 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 identification and design of novel folds.
Keywords protein structure,
Date Deposited 2010-08-27T18:38:28Z
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VAL60    148 views   48 downloads View File Details
Collection of 30063 files in PDB-format, each containing all-atom structural data for the conformation of a polyvaline molecule with 60 residues. All conformations where computer-generated by means of meta-dynamics.
Download: VAL60.zip ( 405.1Mb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


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