"Bioinformatics"

0 Introduction:
0.1 Background:
0.2 Databases:
0.3 Research Groups:
Virginia Bioinformatics Institute
NCBI
PIR
1 Drugs and Targets:
1.1 Drug Structure Format:
Drug Structure File Formats
Drug Structure SMILES Format
Drug Structure File Format Converter
1.2 Databases:
Database: PubChem
Database: DrugBank
Database: DrugBank Search by SMILES
Database: DrugBank Advanced Search
Database: DiTaD
Database: DiTaD Search
ADMET: Open Access ADME/PK Database
ADMET: OCHEM Database
Database: TTD Therapeutic Target Database
Database: The Binding Database
1.3 Research Groups:
OpenBabel
2 Biological Networks:
2.1 Network Format:
BioPAX wiki
BioPAX - Biological Pathway Exchange
Systems Biology Markup Language (SBML) wiki
Systems Biology Markup Language (SBML)
System Biology Format Converter
2.2 Databases:
Database: KEGG
Database: MetaCyc
Database: BIB: Yeast Biological Interaction Browser
Database: UniPathway
TRANSFAC
Transcription Regulatory Regions Database
Database of Interacting Proteins
Biological General Repository for Interaction Datasets (BioGRID)
Database of Interacting Proteins
2.3 Softwares:
Cytoscape
CFinder
MAVisto (Motif Analysis and Visualisation Tool)
Virtual Cell Modeling & Analysis Software
VANTED - Visualization and Analysis of Networks containing Experimental Data
MetNet3D
Modeling in Biology
2.4 Research Groups:
OpenBabel
3 Diseases:
3.1 Diseases:
International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10) Version for 2010
3.2 Disease Databases:
Online Mendelian Inheritance in Man
Genetic Association Database
The Cancer Genome Project
Disease Ontology
The Human Gene Mutation Database
GeneCards V3
3.2 Disease Network Visualization:
The human disease network
Exploring the human diseasome: the human disease network
Network-based global inference of human disease genes
The implications of human metabolic network topology for disease comorbidity
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases
3.3 Research Groups:
OpenBabel
4 DNA, RNA and Protein Sequence Information Resources:
4.1 Introduction:
4.1.1 DNA:
Nucleic acid sequence
GenBank
DDBJ
EMBL
4.1.2 Protein:
Peptide sequence
Protein Information Resource
4.2 Databases:
4.2.1 DNA Databases:
GenBank
DDBJ
EMBL
4.2.2 Protein Databases:
PIR
4.3 Searching:
4.3.1 DNA Databases:
GenBank Entrez
4.3.2 Protein Databases:
PIR Searching
4.4 Research Groups:
OpenBabel
5 Sequence alignment:
5.1 Sequence alignment:
Sequence alignment
Multiple sequence alignment
5.2 Softwares:
EBI BLAST
GenBank BLAST
Sequence alignment software
ClustalW / ClustalX
5.3 Research Groups:
OpenBabel
6 Molecular Evolution:
6.1 Molecular evolution:
Molecular evolution
Computational phylogenetics
6.2 Softwares:
List of phylogenetics software
392 phylogeny packages and 54 free web servers
List of phylogenetics software via expasy
List_of_phylogenetic_tree_visualization_software
Phylogenetic tree viewer
The evolution of modularity in bacterial metabolic networks
6.3 Research Groups:
OpenBabel
7 Gene Annotation and Functional Classification:
7.1 Gene Annotation:
Genome annotation
Gene prediction
Encyclopedia of DNA Elements (ENCODE)
List_of_gene_prediction_software
Ensembl
Entrez Gene
Gene ontology
DAVID (the Database for Annotation, Visualization and Integrated Discovery)
7.2 Databases, Gene Set Enrichment Analysis Softwares, and Gene Prediction Tools:
Gene Ontology (GO)
Encyclopedia of DNA Elements (ENCODE)
Human (Homo sapiens) Genome Browser Gateway
ENSEMBL
KEGG
DAVID (the Database for Annotation, Visualization and Integrated Discovery)
Onto-Tools
7.3 Research Groups:
OpenBabel
8 Proteomics:
8.1 Proteomics:
Proteomics
PRIDE (PRoteomics IDEntifications database)
8.2 Databases:
Proteomics
PRoteomics IDEntifications database (PRIDE)
Proteopedia
8.3 Research Groups:
OpenBabel
9 Analysis of Protein Structure:
9.1 Introduction:
Protein
Protein structure
PDBWiki
Protein Data Bank (PDB)
Worldwide Protein Data Bank
Structural Classification of Proteins (SCOP)
CATH
Pfam
PROSITE
9.2 Databases:
Annotation of protein structures in Structural genomics
Proteopedia
The Human Protein Atlas project
UniProt
Proteins: Biogenesis to Degradation
HUMAN PROTEINPEDIA
PDBe
PDBj
PDB
Structural Classification of Proteins (SCOP)
CATH
Pfam
PROSITE
Protein structure prediction
9.3 Softwares:
PyMOL
SCRATCH Protein structure prediction suite
Structure Prediction Flowchart
9.4 Research Groups:
OpenBabel

2013期末考试文献综述报告
Computational tools for metabolic engineering
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）疾病-基因网络分析
（2）肺癌相关的基因、药物以及靶标网络药理分析
（3）心血管疾病相关的基因、药物以及靶标网络药理分析
（4）萜类化合物生物合成基因、途径与进化分析
（5）细菌代谢网络进化分析
（6）基因组规模基因功能注释方法
（7）基于氨基酸序列的蛋白质结构预测方法
（8）基于氨基酸序列的蛋白质功能预测方法