"计算机辅助药物分子设计"

1.0 Introduction and Marketed Drugs:
Wiki: Drug Design Overview
Wiki: Lipinski's rule of five
1.1 Papers文献:
Lipinski's rule of five (Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings)
The Properties of Known Drugs. 1. Molecular Frameworks
Properties of Known Drugs. 2. Side Chains
Database: PubChem
PubChem: a public information system for analyzing bioactivities of small molecules
Database: DrugBank
DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs
1.2 Practices上机:
1.2.1 Drug Structure Format:
Drug Structure File Formats
Drug Structure SMILES Format
1.2.2 Drug Structure Format Converter:
Drug Structure File Format Converter
1.2.3 Drug Structure Format Test:
....To Be Tested on Class
1.2.4 DrugBank Database:
Database: DrugBank
1.2.5 DrugBank Database Search:
Database: DrugBank Search by SMILES
1.2.6 DrugBank Database Advanced Search:
Database: DrugBank Advanced Search
1.2.7 DiTaD Database:
Database: DiTaD
1.2.8 DiTaD Database Advanced Search:
Database: DiTaD Search
1.2.9 ADMET:
ADMET: Simulation Plus introduction
ADMET: Wiki introduction
ADMET: Open Access ADME/PK Database
ADMET: OCHEM Database

2.0 Targets:
Wiki: Biological target
2.1 Papers文献:
How many drug targets are there?
Trends in the exploitation of novel drug targets.
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery.
2.2 Practices上机:
2.2.1 Therapeutic Target Database Database:
Database: TTD Therapeutic Target Database
2.2.2 DrugBank Database:
Database: DrugBank
2.2.3 The Binding Database:
Database: The Binding Database
2.2.4 DiTaD Database Advanced Search:
Database: DiTaD Search

3.0 Biochemical Reactions:
Wiki: Biochemistry
3.1 Papers文献:
Rhea--a manually curated resource of biochemical reactions.
BKM-react, an integrated biochemical reaction database.
RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.
3.2 Practices上机:
3.2.1 Rhea Database:
Database: Rhea Database
3.2.2 BKM-react Database:
Database: BKM-react
3.2.3 RxnFinder Advanced Search:
Database: RxnDB

4.0 Biological Networks:
Wiki: Biological Networks
Wiki: Metabolic network
Wiki: Metabolic network modelling
Wiki: Protein–protein interaction
Wiki: Gene regulatory network
4.1 Papers文献:
KEGG for integration and interpretation of large-scale molecular data sets.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
UniPathway: a resource for the exploration and annotation of metabolic pathways .
Gene regulatory networks.
A network of protein-protein interactions in yeast.
4.2 Practices上机:
4.2.1 KEGG Database:
Database: KEGG
4.2.2 MetaCyc Database:
Database: MetaCyc
4.2.3 BIB: Yeast Biological Interaction Browser:
Database: BIB: Yeast Biological Interaction Browser
4.2.4 UniPathway Database:
Database: UniPathway
4.2.5 MetNet3D:
Database: MetNet3D

5.0 Quantitative structure–activity relationship models (QSAR models):
Wiki: Quantitative structure–activity relationship
5.1 Papers文献:
External Factor Variable Connectivity Index.
Prediction of Physicochemical Parameters by Atomic Contributions.
Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins
5.2 Practices上机:
5.2.1 3-D QSAR MODELS :
A 3-D QSAR MODELS DATABASE for Virtual Screening
5.2.2 QSAR World!:
QSAR World!
5.2.3 QSAR Main Page:
QSAR Society

6.0 Pharmacophore:
Wiki: Pharmacophore
6.1 Papers文献:
Flexible Alignment of Small Molecules.
6.2 Practices上机:
6.2.1 Pharmacophore Discovery by MOE:
Pharmacophore Discovery by MOE

7.0 Chemical Library Design:
Wiki: Chemical library
7.1 Papers文献:
Rational Methods for the Selection of Diverse Screening Compounds.
7.2 Practices上机:
7.2.1 SYBYL-X: Chemical Library Design by SYBYL-X:
SYBYL-X: Chemical Library Design

8.0 ADMET:
Wiki: ADME
8.1 Papers文献:
Can we estimate the accuracy of ADME-Tox predictions?
8.2 Practices上机:
8.2.1 Open Access ADME/PK Database:
Open Access ADME/PK Database
8.2.2 ADMET and Predictive Toxicology by Discovery Studio:
ADMET and Predictive Toxicology by Discovery Studio

9.0 Docking:
Wiki: Docking (molecular)
9.1 Papers文献:
Docking and scoring in virtual screening for drug discovery: methods and applications
9.2 Practices上机:
9.2.1 AutoDock:
AutoDock
9.2.2 DOCK:
DOCK
9.2.3 Docking by Discovery Studio:
Docking by Discovery Studio
9.2.4 Docking by MOE:
Docking by MOE
9.2.5 Docking by SYBYL-X:
Docking by SYBYL-X

10.0 Virtual screening:
Wiki: Virtual screening
10.1 Papers文献:
Virtual screening – an overview
Virtual screening: an endless staircase?
10.2 Practices上机:
10.2.1 Drug-Target Interaction Prediction:
PreDPI-Ki
10.2.2 Lead Hunting by PreDPI-Ki:
Target-based Hunting (Protein Sequence Needed) to Get Leads
10.2.3 Target Identification by PreDPI-Ki:
Target Identification (Drug Reposition): Drug Structure Needed (as Smiles Strings)
10.2.4 Using AutoDock 4 for Virtual Screening:
Using AutoDock 4 for Virtual Screening
10.2.5 DOCK for Virtual Screening:
DOCK for Virtual Screening
10.2.6 Discovery Studio for Virtual Screening:
Discovery Studio for Virtual Screening
10.2.7 MOE for Virtual Screening:
MOE for Virtual Screening
10.2.8 SYBYL-X for Virtual Screening:
SYBYL-X for Virtual Screening

2013计算机辅助药物分子设计期末考试文献综述报告
要求：PDF文档；采用科学综述论文格式；图表形式列出综述结果；附有文献来源（参考文献）；需要使用教学涉及的技术进行分析。选择如下任一题目：

（1）肺癌相关的基因、药物以及靶标网络药理分析
（2）心血管疾病相关的基因、药物以及靶标网络药理分析
（3）糖尿病相关的基因、药物以及靶标网络药理分析

（4）青蒿素的作用靶标、疾病网络药理分析
（5）紫杉醇的作用靶标、疾病网络药理分析
（6）虫草素的作用靶标、疾病网络药理分析

（7）基于GPCR的药物、疾病网络药理分析
（8）基于GPCR的药物分子设计
（9）针对Alzheimer疾病的药物分子设计