Please anyone suggest for free software for metal complex docking, some software not accepted coordination bond between metal and ligand.
Dear Mohan,
Computational studies on the ligand metal complexes have been performed using HEX 6.3 software which is an interactive molecular graphics program for the interaction, docking calculations, and to identify possible binding site of the biomolecules . The density functional theory (DFT) calculations at B3LYP level were carried out using the GAUSSIAN09 program . The geometries of the complexes optimized using standard 6-31G** basis sets for N, C and H elements and LANL2DZ for metal with effective core pseudo potentials . The coordinates of metal ligand complexes were taken from their optimized structure as a .mol file and were converted to pdb format using GaussView software forever. The default parameters were used for the docking calculation with correlation type shape only, FFT mode at 3D level, grid dimension of 6 with receptor range 180 and ligand range 180 with twist range 360 and distance range. Visualization of the docked systems has been further analyzed with PyMOL software package .
GOLD can dock ligands to proteins with active site metals. Is that what you want? Coordination sites are automatically selected for the metal according to its existing coordination state in the protein,. Alternatively you can force a particular coordination geometry. The docking score (e.g. GOLDscore) then will have a metal binding component which again is metal dependent - though it can be edited if necessary
Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques
October 2017Journal of Computational Chemistry
DOI: 10.1002/jcc.25080
Most docking programs uses the shape based (stereo-electronic fit) approach for generating the complex structures. This approach works best for the ligands (with covalent atomic chemistry) and the proteins.
However, the metal can exhibits entirely different chemistry as compared to the conventional one (oxidation state/partial charge, hydbridisation, geometry, weak electrostatics etc). Therefore, It is very difficult for the normal routine programs to include that huge chemical space of metal and prioritize the best ranking poses. Even though, you can use HexServer, Gold (ensemble docking) and patchdock/Firedock programs to generate the complex; keeping in mind to refine them afterwords for calculating their corrected docking (interaction) energies.
Another approach would be autodock, as it provides the flexibility to incorporate the parameters of your metal in its library file (.gpf/.dpf).
Anyway, research in this field is still going on..
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