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- W3186385648 abstract "Recent advances in technologies like cryoEM structure resolution and protein de novo folding prediction have resulted in a wealth of macromolecular structures that have not been resolved to the level of detail a high-resolution X-ray crystal structure could provide. Taking full advantage of these structures for rational drug design would benefit from additional validation and refinement. In this presentation, we investigate if computational refinement and structure-based modeling methods can be utilized to generate reliable complex poses. We present a solution to the induced fit docking problem for protein−ligand binding by combining ligand-based pharmacophore docking, rigid receptor docking, and protein structure prediction with explicit solvent molecular dynamics simulations. This methodology succeeded in determining protein−ligand binding modes with a root-mean-square deviation within 2.5 A compared to experiment in over 90% of cross-docking cases in our testing. Applications of the predicted ligand-receptor structure in free energy perturbation calculations for additional validation is demonstrated." @default.
- W3186385648 created "2021-08-02" @default.
- W3186385648 creator A5047628202 @default.
- W3186385648 date "2021-06-16" @default.
- W3186385648 modified "2023-09-23" @default.
- W3186385648 title "AI3SD Video: So you predicted a protein structure – What now?" @default.
- W3186385648 doi "https://doi.org/10.5258/soton/p0108" @default.
- W3186385648 hasPublicationYear "2021" @default.
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