Computational and Structural Approaches to Drug Discovery: Ligand–Protein Interactions
Computational methods impact all aspects of modern drug discovery and most notably these methods move rapidly from academic exercises to becoming drugs in clinical trials... This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the factors that determine adsorption, distribution, metabolism, excretion and toxicology are explored, as they remain the critical issues in this area of research. This indispensable resource provides the reader with: * A rich understanding of modern approaches to docking * A comparison and critical evaluation of state-of-the-art methods * Details on harnessing computational methods for both analysis and prediction * An insight into prediction potencies and protocols for unbiased evaluations of docking and scoring algorithms * Critical reviews of current fragment based methods with perceptive applications to kinases Addressing a wide range of uses of protein structures for drug discovery the Editors have created and essential reference for professionals in the pharmaceutical industry and moreover an indispensable core text for all graduate level courses covering molecular interactions and drug discovery.
Computational and Structural Approaches to Drug Discovery: Ligand–Protein Interactions, The Royal Society of Chemistry, 2007.
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Facing the Wall in Computationally Based Approaches to Drug Discoveryp3-23ByJanet S. Finer-Moore;Janet S. Finer-MooreDepartment of Biochemistry and Biophysics, University of California in San FranciscoS412 Genentech Hall, 600 16th StreetSan FranciscoCalifornia94158-2517USASearch for other works by this author on:Jeff Blaney;Jeff BlaneyStructural GenomiX10505 Roselle StreetSan FranciscoCalifornia92121USASearch for other works by this author on:Robert M. StroudRobert M. StroudDepartment of Biochemistry and Biophysics, University of California in San FranciscoS412 Genentech Hall, 600 16th StreetSan FranciscoCalifornia94158-2517USASearch for other works by this author on:
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Chapter 2: The Changing Landscape in Drug Discoveryp24-45ByHugo KubinyiHugo KubinyiD-67256 Weisenheim am SandGermanySearch for other works by this author on:
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Chapter 3: Purine Nucleoside Phosphorylasep49-72ByYang Zhang;Yang ZhangDepartment of Chemistry and Chemical Biology, Cornell UniversityIthacaNY14853USASearch for other works by this author on:Steven E. EalickSteven E. EalickDepartment of Chemistry and Chemical Biology, Cornell UniversityIthacaNY14853USASearch for other works by this author on:
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Chapter 4: Application and Limitations of X-Ray Crystallographic Data in Structure-Guided Ligand and Drug Designp73-94ByAndrew M. Davis;Andrew M. DavisAstraZeneca R&D CharnwoodBakewell RoadLoughborough, Leicestershire LE11 5RHUKSearch for other works by this author on:Simon J. Teague;Simon J. TeagueAstraZeneca R&D CharnwoodBakewell RoadLoughborough, Leicestershire LE11 5RHUKSearch for other works by this author on:Gerard J. KleywegtGerard J. KleywegtDepartment of Cell and Molecular Biology, Uppsala UniversityBiomedical CentreBox 596SE-751 24UppsalaSwedenSearch for other works by this author on:
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Chapter 5: Dealing with Bound Waters in a Site: Do they Leave or Stay?p95-110ByDonald Hamelberg;Donald HamelbergHoward Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of PharmacologyUniversity of California at San DiegoLa JollaCalifornia92093-0365USASearch for other works by this author on:J. Andrew McCammonJ. Andrew McCammonHoward Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of PharmacologyUniversity of California at San DiegoLa JollaCalifornia92093-0365USASearch for other works by this author on:
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Chapter 6: Knowledge-Based Methods in Structure-Based Designp111-126ByMarcel L. Verdonk;Marcel L. VerdonkAstex Therapeutics Ltd.436 Cambridge Science ParkMilton RoadCambridgeCB4 0QAUKSearch for other works by this author on:Wijnand T. M. MooijWijnand T. M. MooijAstex Therapeutics Ltd.436 Cambridge Science ParkMilton RoadCambridgeCB4 0QAUKSearch for other works by this author on:
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Chapter 7: Combating Drug Resistance – Identifying Resilient Molecular Targets and Robust Drugsp127-133ByCelia A. SchifferCelia A. SchifferDepartment of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterMassachusettsUSASearch for other works by this author on:
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Chapter 8: Docking Algorithms and Scoring Functions; State-of-the-Art and Current Limitationsp137-154ByGregory L. Warren;Gregory L. WarrenComputational, Analytical, and Structural SciencesGlaxoSmithKline Pharmaceuticals1250 S. Collegeville Rd.Collegeville PAUSASearch for other works by this author on:Catherine E. Peishoff;Catherine E. PeishoffComputational, Analytical, and Structural SciencesGlaxoSmithKline Pharmaceuticals1250 S. Collegeville Rd.Collegeville PAUSASearch for other works by this author on:Martha S. HeadMartha S. HeadComputational, Analytical, and Structural SciencesGlaxoSmithKline Pharmaceuticals1250 S. Collegeville Rd.Collegeville PAUSASearch for other works by this author on:
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Chapter 9: Application of Docking Methods to Structure-Based Drug Designp155-180ByDemetri T. MoustakasDemetri T. MoustakasDepartment of Chemistry and Chemical Biology, Harvard UniversityCambridge MAUSASearch for other works by this author on:
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Chapter 10: Strength in Flexibility: Modeling Side-Chain Conformational Change in Docking and Screeningp181-191ByLeslie A. KuhnLeslie A. KuhnDepartments of Biochemistry & Molecular Biology, Computer Science & Engineering, and Physics & Astronomy, and the Quantitative Biology and Modeling Initiative502C Biochemistry BuildingMichigan State UniversityEast LansingMichigan48824USASearch for other works by this author on:
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Chapter 11: Avoiding the Rigid Receptor: Side-Chain Rotamersp192-203ByAmy C. AndersonAmy C. AndersonDepartment of Pharmaceutical Sciences, University of Connecticut69 N. Eagleville Rd.StorrsCT 06269USASearch for other works by this author on:
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Chapter 12: Computational Prediction of Aqueous Solubility, Oral Bioavailability, P450 Activity and hERG Channel Blockadep207-222ByDavid E. ClarkDavid E. ClarkArgenta Discovery Ltd.8/9 Spire Green CentreFlex MeadowHarlowEssexCM19 5TRUKSearch for other works by this author on:
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Chapter 13: Shadows on Screensp223-241ByBrian K. Shoichet;Brian K. ShoichetDepartment of Pharmaceutical Chemistry & Graduate Group in Chemistry and Chemical Biology, University of CaliforniaSan Francisco 1700 4th St.Byers Hall Room 508DSan FranciscoCA 94158USASearch for other works by this author on:Brian Y. Feng;Brian Y. FengDepartment of Pharmaceutical Chemistry & Graduate Group in Chemistry and Chemical Biology, University of CaliforniaSan Francisco 1700 4th St.Byers Hall Room 508DSan FranciscoCA 94158USASearch for other works by this author on:Kristin E. D. CoanKristin E. D. CoanDepartment of Pharmaceutical Chemistry & Graduate Group in Chemistry and Chemical Biology, University of CaliforniaSan Francisco 1700 4th St.Byers Hall Room 508DSan FranciscoCA 94158USASearch for other works by this author on:
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Chapter 14: Iterative Docking Strategies for Virtual Ligand Screeningp242-267ByAlbert E. Beuscher IV;Albert E. Beuscher IVMolecular Graphics Laboratory, Department of Molecular Biology, The Scripps Research Institute10550 North Torrey Pines RoadMB-05La JollaCA 92037-1000USASearch for other works by this author on:Arthur J. OlsonArthur J. OlsonMolecular Graphics Laboratory, Department of Molecular Biology, The Scripps Research Institute10550 North Torrey Pines RoadMB-05La JollaCA 92037-1000USASearch for other works by this author on:
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Chapter 15: Challenges and Progresses in Calculations of Binding Free Energies – What Does it Take to Quantify Electrostatic Contributions to Protein–Ligand Interactions?p268-290ByMitsunori Kato;Mitsunori KatoUniversity of Southern California, Department of ChemistryLos AngelesCA90089-1062USASearch for other works by this author on:Sonja Braun-Sand;Sonja Braun-SandUniversity of Southern California, Department of ChemistryLos AngelesCA90089-1062USASearch for other works by this author on:Arieh WarshelArieh WarshelUniversity of Southern California, Department of ChemistryLos AngelesCA90089-1062USASearch for other works by this author on:
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Chapter 16: Discovery and Extrapolation of Fragment Structures towards Drug Designp293-318ByAlessio Ciulli;Alessio CiulliUniversity Chemical LaboratoryLensfield RoadCambridgeCB2 1EWUKSearch for other works by this author on:Tom L. Blundell;Tom L. BlundellDepartment of Biochemistry80 Tennis Court RoadCambridgeCB2 1GAUKSearch for other works by this author on:Chris AbellChris AbellUniversity Chemical LaboratoryLensfield RoadCambridgeCB2 1EWUKSearch for other works by this author on:
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Chapter 17: A Link Means a Lot: Disulfide Tethering in Structure-Based Drug Designp319-348ByJeanne A. HardyJeanne A. HardyThe University of Massachusetts Amherst, Department of Chemistry710 N. Pleasant St.Amherst, MA 01003USASearch for other works by this author on:
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Chapter 18: The Impact of Protein Kinase Structures on Drug Discoveryp349-365BySung-Hou KimSung-Hou KimDepartment of ChemistryUniversity of CaliforniaBerkeley CAUSASearch for other works by this author on:
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