Rational Drug Design. Novel Methodology and Practical Applications

Content: Overview of rational drug design / M. Rami Reddy and Abby L. Parrill Conformational and energetic aspects of receptor-ligand recognition / J.D. Hirst, B. Dominy, Z. Guo, M. Vieth, and C.L. Brooks New free energy calculation methods for structure-based drug design and prediction of protein stability / Lu Wang, Mats A.L. Eriksson, Jed Pitera, and Peter A. Kollman Binding evaluation using the finite difference solution to the linearized Poisson-Boltzmann equation and solvation entropy correction / Jian Shen SmoG, a ligand design method based on knowledge-based parametrization of a solvent reorganization model / Robert S. DeWitte and Eugene I. Shakhnovich The evaluation of multi-body dynamics for studying ligand-protein interactions : using MBO(N)D to probe the unbinding pathways of Cbz-Val-Phe-Phe-Val-Cbz from the active site of HIV-1 protease / Donovan Chin, David N. Haney, Katya Delak, Hon M. Chun, and Carlos E. Padilla Calculation of relative hydration free energy differences for heteroaromatic compounds : use in the design of AMP deaminase inhibitors / Mark D. Erion and M. Rami Reddy New tools for rational drug design / Gregory D. Hawkins, Jiabo Li, Tianhai (Tony) Zhu, Candee C. Chambers, David J. Giesen, Daniel A. Liotard, Christopher J. Cramer, and Donald G. Truhlar Rational Approaches to inhibition of human osteoclast cathepsin K and treatment of osteoporosis / Sherin S. Abdel-Meguid, Baoguang Zhao, Ward W. Smith, Cheryl A. Hanson, Judith LaLonde, Thomas Carr, Karla D'Alessio, Michael S. McQueney, H.-J. Oh, Scott K. Thompson, Daniel F. Veber, and Dennis S. Yamashita Building a hypothesis for nucleotide transport inhibitors / K. Raghavan, Scott D. Kahn, and John K. Buolamwini Unified pharmacophoric model for cannabinoids and aminoalkylindoles derived from molecular superimposition of CB₁ cannabinoid receptor agonists CP55244 and WIN55212-2 / Joong-Youn Shim, Elizabeth R. Collantes, William J. Welsh, and Allyn C. Howlett Structure-based design of novel conformationally restricted HIV protease inhibitors / B.G. Rao, C.T. Baker, J.T. Court, D.D. Deininger, J.P. Griffith, E.E. Kim, J.L. Kim, B. Li, S. Pazhanisamy, F.G. Salituro, W.C. Schairer, and R.D. Tung "New tricks for an old dog" : development and application of novel QSAR methods for rational design of combinatorial chemical libraries and database mining / A. Tropsha, S.J. Cho, and W. Zheng Molecular hologram QSAR / Trevor W. Heritage and David R. Lowis Adapting structure-based drug design in the paradigm of combinatorial chemistry and high-throughput screening : an overview and new examples with important caveats for newcomers to combinatorial library design using pharmacophore models or multiple copy simultaneous search fragments / Arup K. Ghose, Veharkad N. Viswanadhan, and John J. Wendoloski The basic shape topology of protein interfaces / John Lawton, Melanie Tudor, and W. Todd Wipke Evolutionary algorithms in computer-aided molecular design : a review of current applications and a look to the future / David E. Clark Further development of a genetic algorithm for ligand docking and its application to screening combinatorial libraries / Gareth Jones, Peter Willett, Robert C. Glen, Andrew R. Leach, and Robin Taylor Reduced dimensionality in ligand-protein structure prediction : covalent inhibitors of serine proteases and design of site-directed combinatorial libraries / Daniel K. Gehlhaar, Djamal Bouzida, and Paul A. Rejto Development and validation of the EVA descriptor for QSAR studies / David B. Turner, Peter Willett, Allan M. Ferguson, and Trevor W. Heritage PRO_ANALOG, automated analog building according to principles of medicinal chemistry / Richard G.A. Bone, Michael A. Firth, Richard A. Sykes, Christopher W. Murray, and Jin Li Is rational design good for anything? / Donald B. Boyd.

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