Comput Biol Chem - Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

Tópicos

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Resumo

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling.

Resumo Limpo

altern common templat base protein structur predict method base mainchain posit novel sidechain centric approach develop togeth bayesian loop model procedur combin score function stone soup algorithm appli casp set templat base model target although method generat larg perturb templat structur necessari analysi result give uniqu insight differ pack target structur templat consider variat pack found target templat structur even structur close variat found due bodi pack interact outsid inher restrict pack represent pdb first step correct defin region variabl pack map primarili local interact pack secondari tertiari structur larg conserv score function use loop score function base water structur exhibit promis discrimin result present clear structur path develop sidechain center approach templat base model

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