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Endocytobiology III (Annals of the New York Academy of by John J. & Jerome F. Fredrick (editors) LEE

By John J. & Jerome F. Fredrick (editors) LEE

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Extra resources for Endocytobiology III (Annals of the New York Academy of Sciences, 503)

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The scoring function of FlexX is a modification of Böhm’s function developed for the de novo design program LUDI. 6 shows details of the interaction between a ligand and a receptor, obtained from FlexX molecular docking. DOCK DOCK is a simple minimization program that generates many possible orientations of a ligand within a user selective region of the receptor. DOCK is a program for locating feasible binding orientations, given the structures of a “ligand” molecule and a “receptor” molecule [69].

The interaction sites are defined by the distance R, angle α, and dihedral angle ω. The fragments from a 3D database of small molecules are then searched for positioning into suitable interaction sites such that hydrogen bonds can be formed and hydrophobic pockets filled with hydrophobic groups. The suitably oriented fragments are then connected together by spacer fragments to the respective link sites to form the entire molecule. 7 shows LUDI generated fragment interaction sites inside the iNOS substrate binding domain.

Calculatable descriptors like molecular weight, number of rotatable bonds, and log P. Developments in physical organic chemistry over the years and contributions of Hammett and Taft in correlating the chemical activity to structure laid the basis for the development of the QSAR paradigm by Hansch and Fujita. 2 gives an overview of various QSAR approaches in practice. The 2D and 3D QSAR approaches are commonly used methods, but novel ideas are being implemented in terms of 4D–6D QSAR. The increased dimensionality does not add any additional accuracy to the QSAR approach; for example, no claim is valid which states that the correlation developed using 3D descriptors is better than that based on 2D descriptors.

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