課程名稱 |
計算藥物學 Pharmacoinformatics |
開課學期 |
102-2 |
授課對象 |
學程 分子醫藥學程 |
授課教師 |
林榮信 |
課號 |
PHARM5020 |
課程識別碼 |
423 U1480 |
班次 |
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學分 |
3 |
全/半年 |
半年 |
必/選修 |
選修 |
上課時間 |
星期二6,7,8(13:20~16:20) |
上課地點 |
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備註 |
上課地點:水森館(林森南路33號)326室。 總人數上限:45人 |
Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1022PHARM5020_ |
課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
課程大綱
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課程概述 |
一、課程簡介:
Computational Drug Discovery and Design
Successful Examples using Computational Approaches for Drug Design
HIV-protease
Cytochrome P450
G-protein coupled receptors
FKBP
Molecular Interactions
Coulomb Interactions
Van der Waals Interactions
Hydrogen Bonds
Covalent Bonds
Electrostatics in solution
Hydrodynamic Interactions
Modeling Biological Macromolecules
Force Field Formalism
Water
Ions
Amino Acids, Peptides, and Proteins
Nucleic Acids, RNA, and DNA
Lipids
Polarizable Force Fields
Quantum Mechanics/Molecular Mechanics (QM/MM) Approaches
Sampling Phase Spaces of Biomolecules
Monte Carlo Methods
Importance Sampling
Markovian Chain and the Master Equation
Metropolis Algorithm
Molecular Dynamics Methods
Newtonian Equation of Motion
Extension from NVE to NPT ensemble
Limitation of the Time Scale
Hybrid Methods
Docking as a Global Optimization Problem
Designing the Score Function
Binding Affinity
Free Energy Evaluation
Simulated Annealing
Genetic Algorithm
Original Formalism
Lamarckian Genetic Algorithm
Neural Network
Receptor Flexibility and the Relaxed Complex Scheme
SAR by NMR
the tether method
Pharmacophore Mapping
Three Dimensional Quantitative Structure-Activity Relationships (3D-QSAR)
Identification of Pharmacophores
Dynamic Pharmacophore Methods
Toward Virtual Screening of Compounds
Evaluating Structures obtained from Experimental Approaches
Protein Structure Prediction
Protein Folding Kinetics
Drug Library Design and Use of FDA Databases
Lead Finding and Optimization
Rapid Permeability Screening and Predictive ADME
Computational Toxicology
Computational Genomics and Proteomics
Identification and Prediction of Genes
Use of SNP Pharmacogenetics for Drug Design
二、先修課程:
Physical Chemistry, General Physics |
課程目標 |
本課程目標在提供藥物計算的基礎理論背景 |
課程要求 |
待補 |
預期每週課後學習時數 |
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Office Hours |
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指定閱讀 |
待補 |
參考書目 |
Leach, Andrew R. (2001). Molecular Modeling, Second Edition Addison Wesley Longman
Szabo, Attila and Ostlund Neil S. (1990) Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory
Hill, Terrell L., (1986). An Introduction to Statistical Thermodynamics, Dover Publications, Inc. |
評量方式 (僅供參考) |
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週次 |
日期 |
單元主題 |
第1週 |
2/18 |
Course Overview |
第2週 |
2/25 |
Basic Structural Biology and Molecular Graphics |
第3週 |
3/04 |
Ligand Docking and Scoring |
第4週 |
3/11 |
Chemical Databases and Virtual Screening |
第5週 |
3/18 |
Elementary Quantum Chemistry |
第6週 |
3/25 |
Force Field Molecular Mechanics |
第7週 |
4/01 |
Systems of Molecular Simulations |
第8週 |
4/08 |
Energy Minimization |
第9週 |
4/15 |
Mid-term Exam |
第10週 |
4/22 |
Molecular Dynamics and Monte Carlo Methods |
第11週 |
4/29 |
Conformational Analysis |
第12週 |
5/06 |
Clustering Analysis |
第13週 |
5/13 |
Free Energy Evaluation and Computational Alchemy |
第14週 |
5/20 |
Potential of Mean Force Calculations |
第15週 |
5/27 |
Pharmacophore and 3D-QSAR Analysis |
第16週 |
6/03 |
Coarse-Grained Simulations and Formulation Design |
第17週 |
6/10 |
Reports on Term Projects |
第18週 |
6/17 |
Final Exam |
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