山东大学医学院：《生物信息学 Bioinformatics》课程教学资源（PPT课件讲稿）第六章 蛋白质结构预测与分析（蛋白质三级结构、分子表面性质）

CRC Cancer Research Center ANT 1901 Shandong University 第六章 蛋白质结构 预测&分析 2

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CRCI Cancer Research Center Shandong University 633蛋白质三级结构:如何获取 实验方法 计算方法 a houre

实验方法 计算方法 6.3.3 蛋白质三级结构：如何获取 3

CRCI Cancer Research Center Shandong University 633蛋白质三级结构:实验方法获取 X射线衍射法 核磁共振法 冷冻电子显微镜技术 X-ray Crystallography Nuclear Magnetic Resonance(NMR) Cryoelectron Microscopy 94998 9806 650 3PDB PROTEIN DATA BANK

核磁共振法 Nuclear Magnetic Resonance (NMR) 94998 9806 X射线衍射法 X-ray Crystallography 冷冻电子显微镜技术 Cryoelectron Microscopy 650 6.3.3 蛋白质三级结构：实验方法获取 4

CRCI Cancer Research Center Shandong University 633蛋白质三级结构:实验方法获取 X射线衍射法 核磁共振法 X-ray Crystallography Nuclear magnetic Resonance NMR) 5

X射线衍射法 X-ray Crystallography 核磁共振法 Nuclear Magnetic Resonance (NMR) 6.3.3 蛋白质三级结构：实验方法获取 5

CRc Cancer Research Center Shandong University 634蛋白质三级结构:计算方法获取 ey Zero Ccet MEAKIVKVLDSSRCEDGFGKKRKRAASYAAYVTGV SCAKLQNVPPPNGQCQIPDKRRRLEGENKLSAYE NRSGKALVRYYTYEKKTGIAKRVMMYENGEWNDL PEHVCAIQNELEEKSAAIEFKLCGHSFILDFLHMQR LDMETGAKTPLAWIDNAGKCFFPEIYESDERTNYC HHKCVEDPKQNAPHDIKLRLEIDVNGGETPRLNLE ECSDESGDNMMDDVPLAQRSSNEHYDEATEDSC RKLEAAVSKWDETDAVSGAKLTGSEVLDKDAV KKMFAVGTASLGHVPVDVGRFSSEIAEARLALFQ KQVEITKKHRGDANVRYAWLP AKREVSAVMMQG LGVGGAFIRKSIYGVGIHLTAADCPYFSARYCDVDE NGVRYMCRVMGN MELLRGDKAQFFSG GEE YD NGVDDIESPKNYIWNINMNTHIFPEFWVRFKLSNL NAEGNLlAKRDNSGVTLEGPKDLPPQLESNQGAR GSGSANSVGSSTTRPKSPWMPFPTLFAAISHKVAE NDMLLINADYQQLRDKKMTRAEFVRKLRVVGDDL LRSTITTLQNQPKSKEIPGSIRDHEEGAGGL input output 7

MEAKIVKVLDSSRCEDGFGKKRKRAASYAAYVTGV SCAKLQNVPPPNGQCQIPDKRRRLEGENKLSAYE NRSGKALVRYYTYFKKTGIAKRVMMYENGEWNDL PEHVICAIQNELEEKSAAIEFKLCGHSFILDFLHMQR LDMETGAKTPLAWIDNAGKCFFPEIYESDERTNYC HHKCVEDPKQNAPHDIKLRLEIDVNGGETPRLNLE ECSDESGDNMMDDVPLAQRSSNEHYDEATEDSC SRKLEAAVSKWDETDAIVVSGAKLTGSEVLDKDAV KKMFAVGTASLGHVPVLDVGRFSSEIAEARLALFQ KQVEITKKHRGDANVRYAWLPAKREVLSAVMMQG LGVGGAFIRKSIYGVGIHLTAADCPYFSARYCDVDE NGVRYMVLCRVIMGNMELLRGDKAQFFSGGEEYD NGVDDIESPKNYIVWNINMNTHIFPEFVVRFKLSNL PNAEGNLIAKRDNSGVTLEGPKDLPPQLESNQGAR GSGSANSVGSSTTRPKSPWMPFPTLFAAISHKVAE NDMLLINADYQQLRDKKMTRAEFVRKLRVIVGDDL LRSTITTLQNQPKSKEIPGSIRDHEEGAGGL input output 6.3.4 蛋白质三级结构：计算方法获取 7

CRc Cancer Research Center Shandong University 634蛋白质三级结构:计算方法获取 从头计算法 PhysICs 建户 同源建模法 穿线法 综合法 Protein fold recognition 0: 9。 8 L SEGE

⚫ 从头计算法 ⚫ 同源建模法 ⚫ 穿线法 ⚫ 综合法 6.3.4 蛋白质三级结构：计算方法获取 8

CRc Cancer Research Center Shandong University 6341计算方法获取:同源建模法 √原理-相似的氨基酸序列对应着相似的蛋白质结构。 Fapiddynal Retinoic Acid-Binding Protein Plasna Retinol Binding Protei Hilin (bertin IX, Binding Protein Cellalar Ratinol Bulg Poon is sUTa leee 9

✓原理 –相似的氨基酸序列对应着相似的蛋白质结构。 6.3.4.1 计算方法获取：同源建模法 9

CRc Cancer Research Center Shandong University 6341计算方法获取:同源建模法 √预测工具-Swiss-modeLhttp:/swissmodel.expasy.org區 SWISS-MODEL Modelling Tools Repository Documentation Log in Create Account Welcome to sWIss-MODEL SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView(Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide Start Modelling " SWISS-MODEL: modelling protein tertiary and quatemary structure using evolutionary information" has been accepted in Nucleic Acids Research web server issue. You can download the abstract, full text or PDF Protein Structure SWISS- MODEL做出来的结果可以在SCI刊物论文 Bioinformatics Group c/o Prof Torsten Schwede 上作为一项结果来发表,但前提条件是模板与目 Swiss Institute of Bioinformatics 标的序列 identity-要足够高,至少高于30%,因为 。| SWISS-MODEL是单纯的同源建模法,基本居于 CH-4056 Basel/ Switzerland 结构预测软件里的“傻瓜机” 10 help-swissmodel@unibas ch

✓预测工具 –SWISS-MODEL http://swissmodel.expasy.org SWISS-MODEL做出来的结果可以在SCI刊物论文 上作为一项结果来发表，但前提条件是模板与目 标的序列identity要足够高，至少高于30%，因为 SWISS-MODEL是单纯的同源建模法，基本属于 结构预测软件里的“傻瓜机”。 6.3.4.1 计算方法获取：同源建模法 10

CRc Cancer Research Center Shandong University 6341计算方法获取:同源建模法 √预测工具- SWISS-MODEL SWISS-MODEL Modelling Tools Repository Documentation Log in Create Account start a New Modelling project o 结果需在线等3-~5分钟 Target Sequence >test Supported Inputs o (Format must be Fasta KFYFHLMLLAGCIKYGRGENTYDAFVIYSSQDEDWVRNELVKNLEEG Clustal Promod Sequence IPGVAIAANIIHEGFHKSRKVIVVVSQHFIQSRWGTEDVTTAATWAF string, or a valid KVEKTLLRQQVELYRLLSRNTYLEWEDSWLCRHIF/ Uniprot AC otB AC) WQEATSI Target-Template Alignment t Upload Target Sequence File. Swiss Model fasta Upload Template Project Title Deepview Proje Email youremail@sdu.edu.cn 什么都不用自己操心,只输 可人工 入 EMAIL、项目名称和目标 筛选模 Search For Templates Build Model 序列,点 Build Model、OKl 版序列 By using the SWISS-MODEL server, you agree to comply with the following terms of use and cite the corresponding articles

✓预测工具 –SWISS-MODEL 什么都不用自己操心，只输 入EMAIL、项目名称和目标 序列，点Build Model，OK！ 可人工 筛选模 版序列 结果需在线等3~5分钟 6.3.4.1 计算方法获取：同源建模法 11

E All Projects Test Created: today at 11:18 返回结果:返回三个预测模型 Summary Templates(45)Models 3 Model Results o Order by: GMQE Oligo-State Ligands MONOMER(matching None 060447v Template Seq Identity Description 3j0a. 1.A 26.71% Toll-like receptor 5 Model 03 Model-Template Alignment Oligo-State Ligands GMQE OMEAN4 MONOMER None 060-4.67v 自 Detach Reset Template Seq Identity Description 1fyv.1.A 36. 18% TOLL-LIKE RECEPTOR 1 Model 02. Model-Template Alignment Oligo-State Ligands MOE OMEAN4 MONOMER 060-478吧v Template Seq Identity Description 1fyx1A 39.46% TOLL-LIKE RECEPTOR 2 12 Model 01 Model-Templa Ignment

返回结果：返回三个预测模型 12