Download Structural / functional databases of proteins

Computer Aided Drug Design
—— Structural / functional
databases of proteins
Qin Xu
http://cbb.sjtu.edu.cn/~qinxu/CADD.htm
Course Outline
• Introduction and Case Study
• Drug Targets
– Sequence analysis
– Protein structure prediction
• Homology modeling with Discovery Studio
• Model Evaluations
• Structural databases, structural classification databases,
and structural/functional databases of proteins
– Molecular simulation
• Drug Design
– Combinatorial library
– 3D-QSAR
– Statistical methods
• Molecular Docking
UniProt, Universal Protein Resource
EBI (European Bioinformatics Institute) + SIB (Swiss Institute of Bioinformatics)
UniProt
Kowledgebase
Translated EMBL Nucleotide
Sequence Data Library
PIR, Protein Information Resource
Protein Data Bank
Research Collaboratory for Structural
Bioinformatics，RCSB
Search PDB
Search PDB
CATH
CATH
• C : class
• A: architecture
• T: topology
• H: homologous
superfamily
Search in
CATH
SCOP (structural classification of protein)
• 蛋白质结构(PDB) 38 221
• 类（Class）
• 家族（Family）
• 超家族（Supper family）
• 折叠类型（Fold）
• 蛋白质结构域（protein
domain） 110 800
SCOP2
SWISS-MODEL
BMRB, Biological Magnetic
Resonance Data Bank
Pfam, the Protein Families database
InterPro, Integrated Resources of Proteins
Domains and Functional Sites
Course Outline
• Introduction and Case Study
• Drug Targets
– Sequence analysis
– Protein structure prediction
– Molecular simulation
• Drug Design
– Combinatorial library
– 3D-QSAR
– Statistical methods
• Molecular Docking