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Functional site prediction selects correct protein models.


ABSTRACT: The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to be part of a functional site and this information can be used to select model structures from a variety of alternatives that would correspond to a functional protein.Using a large collection of protein-like decoy models, a score was devised that selected those with predicted functional site residues that formed a cluster. When tested on a variety of small alpha/beta/alpha type proteins, including enzymes and non-enzymes, those that corresponded to the native fold were ranked highly. This performance held also for a selection of larger alpha/beta/alpha proteins that played no part in the development of the method.The use of predicted site positions provides a useful filter to discriminate native-like protein models from non-native models. The method can be applied to any collection of models and should provide a useful aid to all modelling methods from ab initio to homology based approaches.

SUBMITTER: Chelliah V 

PROVIDER: S-EPMC2259414 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Functional site prediction selects correct protein models.

Chelliah Vijayalakshmi V   Taylor William R WR  

BMC bioinformatics 20080101


<h4>Background</h4>The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to be part of a functional site and this information can be used to select model structures from a variety of alternatives that would correspond to a functional protein.<h4>Results</h4>Using a large collection of protein-like decoy models, a score was devised that selected t  ...[more]

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