The full set of grid maps and the flexible part of the receptor are used by AutoDock to guide the docking process of the selected ligands.ĪutoDock's main strengths are (i) receptor flexibility (ii) blind-docking (iii) precalculated grid maps on a binding site (iv) free-energy scoring function based on linear regression analysis, the AMBER force field, and a large set of protein–ligand complexes with known inhibition constants and (v) good correlation between predicted inhibition constants and experimental data. Furthermore, AutoGrid generates an electrostatic potential grid map and a desolvation map. AutoGrid is initially used to calculate the noncovalent energy of interaction between the rigid part of the receptor and a probe atom that is located at various grid points of the lattice. The package consists of two sequentially applied programs, AutoGrid and AutoDock. 1996) is the first docking package to model the ligand with full conformational flexibility. Michael Gromiha, in Protein Bioinformatics, 2010 AutoDockĪutoDock ( Morris et al.
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