Abstract

Abstract A shape‐based Gaussian docking function is constructed which uses Gaussian functions to represent the shapes of individual atoms. A set of 20 trypsin ligand–protein complexes are drawn from the Protein Data Bank (PDB), the ligands are separated from the proteins, and then are docked back into the active sites using numerical optimization of this function. It is found that by employing this docking function, quasi‐Newton optimization is capable of moving ligands great distances [on average 7 Å root mean square distance (RMSD)] to locate the correctly docked structure. It is also found that a ligand drawn from one PDB file can be docked into a trypsin structure drawn from any of the trypsin PDB files. This implies that this scoring function is not limited to more accurate x‐ray structures, as is the case for many of the conventional docking methods, but could be extended to homology models. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 76–90, 2003

Keywords

Protein Data Bank (RCSB PDB)Docking (animal)GaussianChemistryProtein Data BankHomology modelingProtein–ligand dockingCrystallographyGaussian functionStereochemistryProtein structureComputational chemistryMolecular dynamicsVirtual screeningEnzymeBiochemistry

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Publication Info

Year
2002
Type
article
Volume
68
Issue
1
Pages
76-90
Citations
487
Access
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Mark McGann, Harold R. Almond, Anthony Nicholls et al. (2002). Gaussian docking functions. Biopolymers , 68 (1) , 76-90. https://doi.org/10.1002/bip.10207

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DOI
10.1002/bip.10207