Li, Hongjian. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (p. 132-156). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract in Chinese --- p.iii / Acknowledgement --- p.iv / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Motivation --- p.2 / Chapter 1.2 --- Objective --- p.2 / Chapter 1.3 --- Method --- p.3 / Chapter 1.4 --- Outline --- p.4 / Chapter 2 --- Background --- p.7 / Chapter 2.1 --- Overview of the Pharmaceutical Industry --- p.7 / Chapter 2.2 --- The Process of Modern Drug Discovery --- p.10 / Chapter 2.2.1 --- Development of an Innovative Idea --- p.10 / Chapter 2.2.2 --- Establishment of a Project Team --- p.11 / Chapter 2.2.3 --- Target Identification --- p.11 / Chapter 2.2.4 --- Hit Identification --- p.12 / Chapter 2.2.5 --- Lead Identification --- p.13 / Chapter 2.2.6 --- Lead Optimization --- p.14 / Chapter 2.2.7 --- Clinical Trials --- p.14 / Chapter 2.3 --- Drug Discovery via Computational Means --- p.15 / Chapter 2.3.1 --- Structure-Based Virtual Screening --- p.16 / Chapter 2.3.2 --- Computational Synthesis of Potent Ligands --- p.20 / Chapter 2.3.3 --- General-Purpose Computing on GPU --- p.23 / Chapter 3 --- Approximate Matching of DNA Patterns --- p.26 / Chapter 3.1 --- Problem Definition --- p.27 / Chapter 3.2 --- Motivation --- p.28 / Chapter 3.3 --- Background --- p.30 / Chapter 3.4 --- Method --- p.32 / Chapter 3.4.1 --- Binary Representation --- p.32 / Chapter 3.4.2 --- Agrep Algorithm --- p.32 / Chapter 3.4.3 --- CUDA Implementation --- p.34 / Chapter 3.5 --- Experiments and Results --- p.39 / Chapter 3.6 --- Discussion --- p.44 / Chapter 3.7 --- Availability --- p.45 / Chapter 3.8 --- Conclusion --- p.47 / Chapter 4 --- Structure-Based Virtual Screening --- p.50 / Chapter 4.1 --- Problem Definition --- p.51 / Chapter 4.2 --- Motivation --- p.52 / Chapter 4.3 --- Medicinal Background --- p.52 / Chapter 4.4 --- Computational Background --- p.59 / Chapter 4.4.1 --- Scoring Function --- p.59 / Chapter 4.4.2 --- Optimization Algorithm --- p.65 / Chapter 4.5 --- Method --- p.68 / Chapter 4.5.1 --- Scoring Function --- p.69 / Chapter 4.5.2 --- Inactive Torsions --- p.72 / Chapter 4.5.3 --- Optimization Algorithm --- p.73 / Chapter 4.5.4 --- C++ Implementation Tricks --- p.74 / Chapter 4.6 --- Data --- p.75 / Chapter 4.6.1 --- Proteins --- p.75 / Chapter 4.6.2 --- Ligands --- p.76 / Chapter 4.7 --- Experiments and Results --- p.77 / Chapter 4.7.1 --- Program Validation --- p.77 / Chapter 4.7.2 --- Virtual Screening --- p.81 / Chapter 4.8 --- Discussion --- p.89 / Chapter 4.9 --- Availability --- p.90 / Chapter 4.10 --- Conclusion --- p.91 / Chapter 5 --- Computational Synthesis of Ligands --- p.92 / Chapter 5.1 --- Problem Definition --- p.93 / Chapter 5.2 --- Motivation --- p.93 / Chapter 5.3 --- Background --- p.94 / Chapter 5.4 --- Method --- p.97 / Chapter 5.4.1 --- Selection --- p.99 / Chapter 5.4.2 --- Mutation --- p.102 / Chapter 5.4.3 --- Crossover --- p.102 / Chapter 5.4.4 --- Split --- p.103 / Chapter 5.4.5 --- Merging --- p.104 / Chapter 5.4.6 --- Drug Likeness Testing --- p.104 / Chapter 5.5 --- Data --- p.105 / Chapter 5.5.1 --- Proteins --- p.105 / Chapter 5.5.2 --- Initial Ligands --- p.107 / Chapter 5.5.3 --- Fragments --- p.107 / Chapter 5.6 --- Experiments and Results --- p.109 / Chapter 5.6.1 --- Binding Conformation --- p.112 / Chapter 5.6.2 --- Free Energy and Molecule Weight --- p.115 / Chapter 5.6.3 --- Execution Time --- p.116 / Chapter 5.6.4 --- Support for Phosphorus --- p.116 / Chapter 5.7 --- Discussion --- p.120 / Chapter 5.8 --- Availability --- p.123 / Chapter 5.9 --- Conclusion --- p.123 / Chapter 5.10 --- Personal Contribution --- p.124 / Chapter 6 --- Conclusion --- p.125 / Chapter 6.1 --- Conclusion --- p.125 / Chapter 6.2 --- Future Work --- p.128 / Chapter A --- Publications --- p.130 / Chapter A.1 --- Conference Papers --- p.130 / Chapter A.2 --- Journal Papers --- p.131 / Bibliography --- p.132
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_327486 |
| Date | January 2011 |
| Contributors | Li, Hongjian., Chinese University of Hong Kong Graduate School. Division of Computer Science and Engineering. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | print, xvi, 156 p. : ill. ; 30 cm. |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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