3D QSAR in Drug Design: Volume 2: Ligand-Protein Interactions and Molecular Similarity
Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin
Springer Science & Business Media, Apr 30, 1998 - Medical - 417 pages
Significant progress has been made in the study of three-dimensional quantitative structure-activity relationships (3D QSAR) since the first publication by Richard Cramer in 1988 and the first volume in the series. 3D QSAR in Drug Design. Theory, Methods and Applications, published in 1993. The aim of that early book was to contribute to the understanding and the further application of CoMFA and related approaches and to facilitate the appropriate use of these methods. Since then, hundreds of papers have appeared using the quickly developing techniques of both 3D QSAR and computational sciences to study a broad variety of biological problems. Again the editor(s) felt that the time had come to solicit reviews on published and new viewpoints to document the state of the art of 3D QSAR in its broadest definition and to provide visions of where new techniques will emerge or new appli- tions may be found. The intention is not only to highlight new ideas but also to show the shortcomings, inaccuracies, and abuses of the methods. We hope this book will enable others to separate trivial from visionary approaches and me-too methodology from in- vative techniques. These concerns guided our choice of contributors. To our delight, our call for papers elicited a great many manuscripts.
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3D QSAR active site algorithm alignment amino acid analogs analysis application approach atomic charges binding affinities binding energies binding free energy bioisosteric Biol biological activity bonds calculations Chem chemical chemistry chemistry-space CoMFA compared complexes compounds Comput conformation correlation database dataset density derived distance diversity drug design ecular effects electron electrostatic potential entropy enzyme EVA descriptor evaluation experimental field-graph flexible force-field G-WHIM Gaussian geometry grid HIV-1 protease hydrogen hydrogen-bond hydrophobic initio interaction energies intermolecular kcal/mol Kohonen Kohonen network ligand maps method metrics molecular dynamics molecular dynamics simulations molecular field molecular mechanics molecular similarity molecular surface molecules neurons obtained optimization parameters peptide pharmacophore Phys prediction properties protease inhibitors protein protein-ligand QM/MM QSAR in Drug quantum receptor regression scoring function semiempirical solvation solvent steric Struct substrate target structure techniques three-dimensional VALIDATE values variables Waals WHIM descriptors X-ray structure