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- W2023277005 abstract "Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a 'corner' architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present 'only' in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign." @default.
- W2023277005 created "2016-06-24" @default.
- W2023277005 creator A5010018908 @default.
- W2023277005 creator A5079363007 @default.
- W2023277005 creator A5086234259 @default.
- W2023277005 date "2010-06-04" @default.
- W2023277005 modified "2023-10-05" @default.
- W2023277005 title "A structural-alphabet-based strategy for finding structural motifs across protein families" @default.
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- W2023277005 doi "https://doi.org/10.1093/nar/gkq478" @default.
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