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genetic algorithm, which is the hybrid of genetic algorithm
and local search algorithm for the conformational search.
For the protein preparation, the PR protein A with
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retrieved from PDB (PDB code: 1ZUC), and structural
basis for androgen specificity and estrogen synthesis in
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from PDB (PDB code: 3EQM). The tanaproget ligand,
sulfate ion (PDB code: 1ZUC), and 4-androstene-3-17-
dione, protoporphyrin IX containing Fe, phosphate ion
(PDB code: 3EQM), and water molecules were removed,
leaving the free receptor. In both proteins, the polar
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selected and calculated for the partial charge. Further, the
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macromolecule. The docking area was assigned visually
around the apparent active site of a grid of 80 × 80 × 80 Å
with a grid spacing of 0.375 Å and positioned around the
active site with all the ligand atom types by using
AutoGrid. All parameters were set to defaults except
ga_run (100). The docking results were clustered on the
basis of rmsd and were ranked on the basis of free energy
of receptor binding. All compounds were drawn and then
converted to 3D by ChemDraw (Cam-bridgesoft Inc,
Waltham, MA). Each structure was then energy minimized
by AM1 force field. The Discovery Studio Visualizer
(Cambridge, UK) was used for 3D visualization [27–30].
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Acknowledgments. The authors gratefully acknowledge BRNS,
India, for financial support; DST for providing HRMS facility;
and CSIR, New Delhi, for awarding JRF to SK and NV.
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Journal of Heterocyclic Chemistry
DOI 10.1002/jhet