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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