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• W2097029677 endingPage "928" @default.
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• W2097029677 abstract "Abstract Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using R OSETTA L IGAND , we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density‐95/Dlg/ZO‐1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately." @default.
• W2097029677 created "2016-06-24" @default.
• W2097029677 creator A5046840321 @default.
• W2097029677 creator A5050843177 @default.
• W2097029677 date "2010-03-30" @default.
• W2097029677 modified "2023-10-16" @default.
• W2097029677 title "A flexible docking scheme to explore the binding selectivity of PDZ domains" @default.
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• W2097029677 doi "https://doi.org/10.1002/pro.366" @default.
• W2097029677 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2868235" @default.
• W2097029677 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20196074" @default.
• W2097029677 hasPublicationYear "2010" @default.

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