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A computational framework for structure-based drug discovery with GPU acceleration.

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

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_327486
Date January 2011
ContributorsLi, Hongjian., Chinese University of Hong Kong Graduate School. Division of Computer Science and Engineering.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, xvi, 156 p. : ill. ; 30 cm.
RightsUse 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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