Computational Drug Discovery and Design

Part I: Drug Binding Site Prediction, Design, and Descriptors1. A Molecular Dynamics Ensemble-based Approach for the Mapping of Druggable Binding SitesAnthony Ivetac and J, Andrew McCammon2. Analysis of Protein Binding Sites by Computational Solvent MappingDavid R. Hall, Dima Kozakov, and Sandor Vajda3. Evolutionary Trace for Prediction and Redesign of Protein Functional SitesAngela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge4. Information Entropic Function for Molecular Descriptor ProfilingAnne Mai Wasswrmann, Britta Nisius, Martin Vogt, andJürgen BajorathPart II: Virtual Screening of Large Compound Libraries: Including Molecular Flexibility5. Expanding the Conformational Selection Paradigm in Protein-Ligand DockingGuray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov6. Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug DesignSimone Fulle and Holger Gohlke7.On the Use of Molecular Dynamics Receptor Conformations for Virtual ScreeningSara Nichols, Riccardo Baron, and J. Andrew McCammon8. Virtual Ligand Screening Against Comparative Protein Structure ModelsHao Fan, John J. Irwin, and Andrej Sali9.AMMOS Software: Method and ApplicationTania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, and Maria A. Miteva10.Rosetta Ligand Docking with Flexible XML ProtocolsGordon Lemmon and Jens Meiler11.Normal Mode-Based Approaches in Receptor Ensemble DockingClaudio N. Cavasotto12. Application of Conformational Clustering in Protein-Ligand DockingGiovanni Bottegoni, Walter Rocchia, and Andrea Cavalli13. How to Benchmark Methods for Structure-based Virtual Screenin of Large Compound LibrariesAndrew J. Christofferson and Niu HuangPart III: Prediction of Protein-Protein Docking and Interactions14. AGGRESCAN: Method, Application, and Perspectives for Drug DesignNatalia S. de Groot, Virginia Castillo, Ricardo Graña, and Salvador Ventura Zamora15. ATTRACT and PTOOLS: Open Source Programs for Protein-protein DockingSebastian Schneider, Adrien Saladin, Chantal Prevost, and Martin Zacharias16. Prediction of Interacting Protein Residues using Sequence and Structure DataVedran Franke, Mile Sikic, and Kristian VlahovicekPart IV: Rescoring Docking Predictions17. MM-GB/SA Rescoring of Docking PosesCristiano R.W. Guimarães18. A Case Study of Scoring and Rescoring in Peptide DockingZunnan Huang and Chung Wong19. The Solvated Interaction Energy (SIE) Method for Scoring Binding AffinitiesTraian Sulea and Enrico Purisima20. Linear Interaction Energy (LIE): Method and Applications in Drug DesignHugo Guitiérrez-de-Terán and Johan ÅqvistPart V: Crucial Neglected Effects: Entropy, Solvent, and Protonation21. Estimation of Conformational Entropy in Protein-Ligand Interactions: A Computational PrespectiveAnton Polyansky, Ruben Zubac, and Bojan Zagrovic22. Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing ApproachPanagotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin23. Protein-water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration SitesArianna Fornili, Flavia Autore, Nesrine Chakroun, Pierre Martinez, and Franca Fraternali24. Computing the Thermodynamic Contributions of Interfacial WaterZheng Li and Themis Lazaridis25. Assignment of Protonation States in Proteins and Ligands: Combining pK a Prediction with Hydrogen Bonding Network OptimizationElmar Krieger, Rob Hooft, Roland Dunbrack, and Barbara KriegerPart VI: Toward the Use of Robust Free Energy Methods in Drug Design26. Best Practices in Free Energy Calculations for Drug DesignMichael Shirts27. Independent-Trajectory Thermodynamic Integration:A Practical Guide to Protein-Drug Binding Fre... Mehr