{ "item_title" : "Computational Drug Discovery and Design", "item_author" : [" Riccardo Baron "], "item_description" : "Part I: Drug Binding Site Prediction, Design, and Descriptors 1. A Molecular Dynamics Ensemble-based Approach for the Mapping of Druggable Binding Sites Anthony Ivetac and J, Andrew McCammon 2. Analysis of Protein Binding Sites by Computational Solvent Mapping David R. Hall, Dima Kozakov, and Sandor Vajda 3. Evolutionary Trace for Prediction and Redesign of Protein Functional Sites Angela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge 4. Information Entropic Function for Molecular Descriptor Profiling Anne Mai Wasswrmann, Britta Nisius, Martin Vogt, and J rgen Bajorath Part II: Virtual Screening of Large Compound Libraries: Including Molecular Flexibility 5. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking Guray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov 6. Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design Simone Fulle and Holger Gohlke 7.On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening Sara Nichols, Riccardo Baron, and J. Andrew McCammon 8. Virtual Ligand Screening Against Comparative Protein Structure Models Hao Fan, John J. Irwin, and Andrej Sali 9.AMMOS Software: Method and Application Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, and Maria A. Miteva 10.Rosetta Ligand Docking with Flexible XML Protocols Gordon Lemmon and Jens Meiler 11.Normal Mode-Based Approaches in Receptor Ensemble Docking Claudio N. Cavasotto 12. Application of Conformational Clustering in Protein-Ligand Docking Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli 13. How to Benchmark Methods for Structure-based Virtual Screenin of Large Compound Libraries Andrew J. Christofferson and Niu Huang Part III: Prediction of Protein-Protein Docking and Interactions 14. AGGRESCAN: Method, Application, and Perspectives for Drug Design Natalia S. de Groot, Virginia Castillo, Ricardo Gra a, and Salvador Ventura Zamora 15. ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking Sebastian Schneider, Adrien Saladin, Chantal Prevost, and Martin Zacharias 16. Prediction of Interacting Protein Residues using Sequence and Structure Data Vedran Franke, Mile Sikic, and Kristian VlahovicekPart IV: Rescoring Docking Predictions17. MM-GB/SA Rescoring of Docking Poses Cristiano R.W. Guimar es 18. A Case Study of Scoring and Rescoring in Peptide Docking Zunnan Huang and Chung Wong 19. The Solvated Interaction Energy (SIE) Method for Scoring Binding Affinities Traian Sulea and Enrico Purisima 20. Linear Interaction Energy (LIE): Method and Applications in Drug Design Hugo Guiti rrez-de-Ter n and Johanqvist Part V: Crucial Neglected Effects: Entropy, Solvent, and Protonation 21. Estimation of Conformational Entropy in Protein-Ligand Interactions: A Computational Prespective Anton Polyansky, Ruben Zubac, and Bojan Zagrovic 22. Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing Approach Panagotis L. Kastritis, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin 23. Protein-water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites Arianna Fornili, Flavia Autore, Nesrine Chakroun, Pierre Martinez, and Franca Fraternali 24. Computing the Thermodynamic Contributions of Interfacial Water Zheng Li and Themis Lazaridis 25. Assignment of Protonation States in Proteins and Ligands: Combining pK a Prediction with Hydrogen Bonding Network Optimization Elmar Krieger, Rob Hooft, Roland Dunbr", "item_img_path" : "https://covers2.booksamillion.com/covers/bam/1/49/396/227/1493962272_b.jpg", "price_data" : { "retail_price" : "169.99", "online_price" : "169.99", "our_price" : "169.99", "club_price" : "169.99", "savings_pct" : "0", "savings_amt" : "0.00", "club_savings_pct" : "0", "club_savings_amt" : "0.00", "discount_pct" : "10", "store_price" : "" } }

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