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- W2344463668 abstract "Predicting the three-dimensional conformation adopted by a protein sequence is an unsolved problem in computational molecular biology. Currently, the best technique for the prediction of structure from sequence is comparative modelling: in all known cases, two evolutionarily-related proteins with similar sequences ($>$30% sequence identity) have similar three-dimensional conformations. A sequence alignment can therefore be used to construct a model for a target sequence, using the coordinates of a related parent sequence for which a structure has already been determined by experimental methods.The predictive power of comparative modelling was objectively assessed by making bona fide predictions for three targets at the first meeting for the Critical Assessment of protein Structure Prediction methods (CASP1) in December, 1994. The results from this meeting show that even though comparative modelling is the best method available to predict structures, the context-sensitivity of interactions in protein structures appears to be a major hurdle preventing the construction of accurate models.We use an algorithm based on graph theory to handle this problem. Each possible residue conformation is represented as a node in a graph. Each node is weighted based on the strength of the interaction between the side chain and the local main chain. Edges are then drawn between nodes in a self-consistent manner, and are weighted based on the strength of the interaction between the two nodes. Once a graph representing all possible conformations and their interactions is constructed, the maximal sets of completely connected nodes (cliques) the size of the protein sequence are found using a clique finding algorithm. The clique with the best weight represents the optimal combination of the main chain and side chain possibilities that are input to the algorithm, and is assumed to represent a correct native-like conformation.We have tested this novel method objectively by making predictions at the second meeting on the Critical Assessment of protein Structure Prediction methods (CASP2) in December, 1996, and find that significant improvements have been made in the building of side chains and main chain regions in comparative modelling." @default.
- W2344463668 created "2016-06-24" @default.
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- W2344463668 date "1998-03-17" @default.
- W2344463668 modified "2023-09-27" @default.
- W2344463668 title "A graph-theoretic solution to the context-sensitivity problem in protein structure prediction" @default.
- W2344463668 hasPublicationYear "1998" @default.
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