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• W2217493032 abstract "Preferred conformations of amino acid side chains have been well established through statistically obtained rotamer libraries. Typically, these provide bond torsion angles allowing a side chain to be traced atom by atom. In cases where it is desirable to reduce the complexity of a protein representation or prediction, fixing all side-chain atoms may prove unwieldy. Therefore, we introduce a general parametrization to allow positions of representative atoms (in the present study, these are terminal atoms) to be predicted directly given backbone atom coordinates. Using a large, culled data set of amino acid residues from high-resolution protein crystal structures, anywhere from 1 to 7 preferred conformations were observed for each terminal atom of the non-glycine residues. Side-chain length from the backbone Cα is one of the parameters determined for each conformation, which should itself be useful. Prediction of terminal atoms was then carried out for a second, nonredundant set of protein structures to validate the data set. Using four simple probabilistic approaches, the Monte Carlo style prediction of terminal atom locations given only backbone coordinates produced an average root mean-square deviation (RMSD) of ∼3 Å from the experimentally determined terminal atom positions. With prediction using conditional probabilities based on the side-chain χ1 rotamer, this average RMSD was improved to 1.74 Å. The observed terminal atom conformations therefore provide reasonable and potentially highly accurate representations of side-chain conformation, offering a viable alternative to existing all-atom rotamers for any case where reduction in protein model complexity, or in the amount of data to be handled, is desired. One application of this representation with strong potential is the prediction of charge density in proteins. This would likely be especially valuable on protein surfaces, where side chains are much less likely to be fixed in single rotamers. Prediction of ensembles of structures provides a method to determine the probability density of charge and atom location; such a prediction is demonstrated graphically." @default.
• W2217493032 created "2016-06-24" @default.
• W2217493032 creator A5020578506 @default.
• W2217493032 creator A5090453372 @default.
• W2217493032 date "2004-02-21" @default.
• W2217493032 modified "2023-09-23" @default.
• W2217493032 title "Statistically Based Reduced Representation of Amino Acid Side Chains" @default.
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• W2217493032 doi "https://doi.org/10.1021/ci034177z" @default.
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