蛋白质的功能与结构预测范例.ppt

基础生物信息学及应用 李裕强 2009.09 第Ⅲ部分生物分子信息的分析 本章内容： 蛋白质家族和结构域数据库 蛋白质功能预测 蛋白质结构预测 第一节 蛋白质家族和结构域数据库 本节内容： 蛋白质模体及结构域数据库 蛋白质家族数据库 蛋白质结构数据库 其它生物大分子数据库 1、蛋白质模体及结构域数据库 模体和结构域 PROSITE数据库 PRINTS数据库 BLOCKS数据库 ProDom数据库 Pfam数据库 SMART数据库 InterPro数据库 Conserved Domain数据库 CDART 蛋白质模体及结构域数据库 模体（motifs）和结构域 （domains）： Biologists can gain insight of the protein function based on identification of short consensus sequences related to known functions. These consensus sequence patterns are termed motifs and domains. A motif is a short conserved sequence pattern associated with distinct functions of a protein or DNA. It is often associated with a distinct structural site performing a particular function. A typical motif, such as a Zn-finger motif, is ten to twenty amino acids long. 蛋白质模体及结构域数据库 A domain is also a conserved sequence pattern, defined as an independent functional and structural unit. Domains are normally longer than motifs. A domain consists of more than 40 residues and up to 700 residues, with an average length of 100 residues. A domain may or may not include motifs within its boundaries. Examples，transmembrane domains， ligand-binding domains. 蛋白质模体及结构域数据库 Identification of motifs and domains heavily relies on multiple sequence alignment as well as profile and hidden Markov model (HMM) construction 蛋白质模体及结构域数据库 PROSITE（蛋白质家族及结构域数据库）： The first established sequence pattern database /prosite/ 是蛋白质家族和结构域数据库，包含具有生物学意义的位点、模式、可帮助识别蛋白质家族的统计特征。 PROSITE中涉及的序列模式包括酶的催化位点、配体结合位点、与金属离子结合的残基、二硫键的半胱氨酸、与小分子或其它蛋白质结合的区域等。 PROSITE还包括根据多序列比对而构建的序列统计特征，能更敏感地发现一个（未知）序列是否具有相应的特征。 The functional information of these patterns is primarily based on published literature. 蛋白质模体及结构域数据库 PRINTS（蛋白质模体指纹数据库）： A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3