Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
442993 | Journal of Molecular Graphics and Modelling | 2007 | 11 Pages |
Abstract
A methodology has been developed for the simulation of induced fit between a ligand and its target protein. It utilizes constrained molecular dynamics where atoms determined to be immobile from difference distance matrix studies are fixed. Application of this methodology to HIV-1 reverse transcriptase (RT) as the example target protein has demonstrated its robustness. Short simulation times are sufficient to achieve good refinement of docking poses resulting from exchange of structurally dissimilar inhibitors between crystal structures.
Related Topics
Physical Sciences and Engineering
Chemistry
Physical and Theoretical Chemistry
Authors
James Garner, John Deadman, David Rhodes, Renate Griffith, Paul A. Keller,