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3D QSAR in Drug Design: Ligand-Protein Interactions and - download pdf or read online

By Tommy Liljefors (auth.), Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin (eds.)

ISBN-10: 0306468573

ISBN-13: 9780306468575

ISBN-10: 0792347900

ISBN-13: 9780792347903

Significant development has been made within the research of three-d quantitative structure-activity relationships (3D QSAR) because the first e-book via Richard Cramer in 1988 and the 1st quantity within the sequence. 3D QSAR in Drug layout. concept, equipment and purposes, released in 1993. the purpose of that early publication used to be to give a contribution to the certainty and the extra software of CoMFA and comparable methods and to facilitate the best use of those tools. considering the fact that then, 1000s of papers have seemed utilizing the quick constructing strategies of either 3D QSAR and computational sciences to review a extensive number of organic difficulties. back the editor(s) felt that the time had come to solicit experiences on released and new viewpoints to record the cutting-edge of 3D QSAR in its broadest definition and to supply visions of the place new strategies will emerge or new appli- tions can be chanced on. The goal is not just to spotlight new principles but in addition to teach the shortcomings, inaccuracies, and abuses of the tools. we are hoping this e-book will allow others to split trivial from visionary techniques and me-too method from in- vative recommendations. those issues guided our selection of participants. To our satisfaction, our demand papers elicited a good many manuscripts.

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Additional info for 3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity

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1. The steric and energetic intermolecular interactions and the steric fit Structural complementarity is essential for the specific binding of a ligand to the receptor at the binding site. The non-bonded steric interaction energy is computed from the explicit sum of the Lennard-Jones potentials: (14) where and rij is the distance between atom center i and atom center j, Ri,εi is the vdW radius, epsilon value of atom i, and Ri, εj is the vdW radius, epsilon value of atom j. The electrostatic interaction energy is the explicit sum of the Coulombic potentials (15) using partial atomic charges on the ligand (qi) and the receptor (qj) from the implementation of the Amber force field within the MacroModel program.

Ligand transfer from solution into the binding site The lipophilicity of a hydrophobe is estimated by the energy needed to create a cavity in the ayucous solvent in which that molecule can tit. When hydrophobic ligands bind to the receptor, the energy of cavity creation is released. entropically favoring the process. Log P, the partition coefficient for octanol-water [67], gauges the ligand's preference for the active site of the receptor versus the aqueous solvent. 1 [ 68] to compute the ligand's partition coefficient.

12 (1993) 9–20. , Chrigadze. D.. Draheim. W , Sommers, C. , structure-based design of the first potent and selective inhibitor of human non-pancreatic secretary PhospholipaseA2, Nat. Struct. , 2 (1995) 458–465. , Cieplak. , Bayly. M.. M.. , Caldwell. W. and Kollman. , A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc.. 117 (1995) 5 179-5197. Gilson. , Sharp. A. and Honig. , Calculating the electrostatic potential of molecules in rolution: Method and error assessment, J.

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3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity by Tommy Liljefors (auth.), Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin (eds.)

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