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50 < 10 μM) have log P values ranging from 2.44 (2a) to 3.57 4a
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50 < 10 μM) have log P values ranging from 2.44 (2a) to 3.57 (4a).
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McMartin, C, Bohacek, R.S. QXP: powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aid.-Mol. Des. 1997, 11, 333-344. The molecular model of 4c was built with the QXP editor and minimized using the default protocol (300 iterations, energy cut-off of 0.1 kJ·mol-1, Polak-Ribiere conjugate gradient, The ligand-free protein and cofactor were kept rigid, except for the side chains of the residues lying within a distance of 4 Å from 1,4-diphenyl-2-butene in the original pdb complex (1oj9) retrieved by the Brookhaven Protein Data Bank http://www.rcsb.org/pdb/, which were settled free to relax during the minimization of the binding complexes found by the calculation routine. Finally, phenol oxygen atom of Y398 was marked for indicating the binding cavity, and the inhibitor added and settled as completely free to move. To allow a good sampling of the conformational space, 1000 runs of Monte Carlo search, followe
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-1, Polak-Ribiere conjugate gradient). The ligand-free protein and cofactor were kept rigid, except for the side chains of the residues lying within a distance of 4 Å from 1,4-diphenyl-2-butene in the original pdb complex (1oj9) retrieved by the Brookhaven Protein Data Bank (http://www.rcsb.org/pdb/), which were settled free to relax during the minimization of the binding complexes found by the calculation routine. Finally, phenol oxygen atom of Y398 was marked for indicating the binding cavity, and the inhibitor added and settled as completely free to move. To allow a good sampling of the conformational space, 1000 runs of Monte Carlo search, followed by conjugate gradient minimization, were performed, and the first-scored 25 low-energy docking hypotheses were taken into account.
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