Ligand docking

DOCK ligand dockiag/active site probe tool I. D. Kunt2 at University of California, San... 

CAChe 5.0, available in 2002, includes a new, more powerful, semiempirical method that uses the PM5 Hamiltonian, a MOPAC 2002 offering, modeling of molecules with up to 20,000 atoms, the inclusion of all main group elements in one semiempirical method, and using MOPAC AMl-d, supports the transition metals Pt, Fe, Cu, Ag, Mo, V, and Pd. Researchers can now import and display, in 3D, proteins from the Protein Data Bank (PDB), optimize proteins, dock ligands, and model reactions on protein molecules. 

DOCKING LIGANDS INTO THE iGluR2 BINDING SITE... 

Several programs have been developed for docking ligands into receptors (see O Table 12-3). These programs differ in the treatment of the ligands and the ranking methods. Efficiency and accuracy are... 

Corbeil, C. R., Moitessier, N. (2009) Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs. J Chem Inf Model 49, 997-1009. 

Run PLCALC to calculate the receptor-ligand interaction (HT) scores (42) for each docked ligand pose in the above output file and output the scored dock poses to an SDF file. 

The binding energy (AEh) of the docked CDNB used to assess the relative affinities of the docked ligand at the H-site of the different GST-pi variants was calculated using the CFF91 force field, according to the method of Robinson et al.31 as shown in Equation 15.2 ... 

The results of an AutoDock run are stored in PDB format. To view the final results, a PDB file containing the complex of all docked poses of the ligand in the protein can be generated using the get-docked utility (see Notes 3 and 8) get-docked LIGAND.protein.dlg... 

CAChe WorkSystem Pro, and BioMedCAChe provide the necessary tools to execute tasks involved in in silico compound screening such as docking, ligand tune-up, etc. MOPAC 2002 s MOZYME now allows the execution of semi-empir-ical calculations of large molecules (proteins, polymers, semiconductors, and crystals) in a quick yet accurate fashion. For the scientists that need to work on molecules whose parameters are either not included in MOPAC 2002 or that need to tune-up particular parameters based on ab initio or experimental data, Fujitsu offers its services to customize parameters on contractual basis. 

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