生物信息学第4章蛋白质序列数据库

生物信息研究中常用蛋白质数据库简述内蒙古工业大学理学院呼和浩特孙利霞2010.1.5摘要：在后基因组时代生物信息学的研究当中，离不开各种生物信息学数据库。

尤其在蛋白质从序列到功能的研究当中，目前各种行之有效的方法都是基于各种层次和结构的蛋白质数据库。

随着计算机技术及网络技术的发展，目前的蛋白质数据库不论是所包含数据量还是功能都日新月异，新的数据库层出不穷。

一个新手面对如此浩瀚的数据量往往无从下手。

本文粗浅地为目前蛋白质数据库的使用勾画出一个轮廓，作为自己蛋白质研究入门的一个引导。

关键词：蛋白质；数据库0 引言随着科技的发展，个人的知识往往赶不上快速膨胀的信息量，人们为了解决这个问题，便创建了形形色色的数据库。

蛋白质数据库是指：在蛋白质研究领域根据实际需要，对蛋白质序列、蛋白质结构以及文献等数据进行分析、整理、归纳、注释，构建出具有特殊生物学意义和专门用途的数据库。

蛋白质数据库总体上可分为两大类：蛋白质序列数据库和蛋白质结构数据库，蛋白质序列数据库来自序列测定，结构数据库来自X-衍射和核磁共振结构测定（详见图1）。

这些数据库是分子生物信息学的基本数据资源。

上世纪90年代，我国从事蛋白质研究的学者使用的蛋白质数据库储存介质还是国外实验室发布的激光光盘[1]。

信息的传播储存甚为不便。

随着蛋白质研究的发展飞快，同时伴随着计算机和因特网发展，蛋白质数据库的储存传播方式也发生的巨大的变化。

进入21世纪后，我们所用的各种蛋白质数据库都发展成为存储在网络服务器上，基于“服务器—客户机”的访问查询方式。

伴随着计算机及物理测试技术的发展数据库的容量和功能成数量级膨胀。

但是面对如此浩瀚的数据，新手往往感到无从下手，在需要时找不到自己需要的合适数据库。

本文从目前蛋白质数据库建立的的逻辑层次出发，系统地简绍了常用蛋白质数据的概况，它们的查询方法以及它们相互之间的联系。

同时尽量不涉及数据库建设和维护方面的计算机和网络这些数据库底层的技术，为蛋白质研究的入门者及对蛋白质感兴趣的人员的一个引导。

蛋白质序列数据库我们可以根据基因组序列预测新基因，预测编码区域，并推测其产物（即蛋白质）的序列。

因此，随着基因组序列的不断增长，蛋白质序列也在不断增加。

PIR历史上，蛋白质数据库的出现先于核酸数据库。

在1960年左右，Dayhoff和其同事们搜集了当时所有已知的氨基酸序列，编著了《蛋白质序列与结构图册》。

从这本图册中的数据，演化为后来的蛋白质信息资源数据库PIR（Protein Information Resource）。

PIR是由美国生物医学基金会NBRF（National Biomedical Research Foundation）于1984年建立的，其目的是帮助研究者鉴别和解释蛋白质序列信息，研究分子进化、功能基因组，进行生物信息学分析。

它是一个全面的、经过注释的、非冗余的蛋白质序列数据库。

所有序列数据都经过整理，超过99%的序列已按蛋白质家族分类，一半以上还按蛋白质超家族进行了分类。

PIR提供一个蛋白质序列数据库、相关数据库和辅助工具的集成系统，用户可以迅速查找、比较蛋白质序列，得到与蛋白质相关的众多信息。

目前，PIR已经成为一个集成的生物信息数据源，支持基因组研究和蛋白质组研究。

至2004年，PIR 有近30万个蛋白质的登录数据项，包括来自不同生物体的蛋白质序列。

除了蛋白质序列数据之外，PIR还包含以下信息：（1）蛋白质名称、蛋白质的分类、蛋白质的来源；（2）关于原始数据的参考文献；（3）蛋白质功能和蛋白质的一般特征，包括基因表达、翻译后处理、活化等；（4）序列中相关的位点、功能区域。

对于数据库中的每一个登录项，有与其它数据库的交叉索引，包括到GenBank、EMBL、DDBJ、GDB、MELINE等数据库的索引。

PIR中一个具体的登录项如图4.4所示。

PIR提供三种类型的检索服务。

一是基于文本的交互式查询，用户通过关键字进行数据查询。

二是标准的序列相似性搜索，包括BLAST、FastA等。

实验四、蛋白质序列分析及结构预测一、用BioEdit等软件进行序列分析打开FASTA格式序列1、Sequence-Protein-Amino Acid Composition分子质量；氨基酸组成Protein: gi|725605238|ref|XM_010330964.1| PREDICTED: Saimiri boliviensis boliviensis interferon, lambda 3 (IFNL3), mRNALength = 248 amino acidsMolecular Weight = 27462.22 DaltonsAmino Acid Number Mol%Ala A 25 10.08Cys C 9 3.63Asp D 13 5.24Glu E 14 5.65Phe F 6 2.42Gly G 10 4.03His H 10 4.03Ile I 3 1.21Lys K 8 3.23Leu L 37 14.92Met M 5 2.02Asn N 4 1.61Pro P 18 7.26Gln Q 10 4.03Arg R 22 8.87Ser S 15 6.05Thr T 16 6.45Val V 15 6.05Trp W 4 1.61Tyr Y 2 0.81氨基酸组成表2、helical wheel diagram3、Hydrophobic Moment matrix with Eisenberg consensus scale 疏水性4、Kyte&Doolittle Mean Hydrophobicity Profile5、Eisenberg Scale Mean Hydrophobicity Profile6、Cornette Scale Mean Hydrophobicity Profile7、Parker HPLC Scale Mean Hydrophobicity Profile8、Boyko Scale Mean Hydrophilicity Profile9、Hopp%Woods Scale Mean Hydrophilicity10、ProtParam tool /protparam/ProtParam (References / Documentation) is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRA VY) (Disclaimer).输入FASTA格式序列等电点11、跨膜区分析进入CBS 依次进入TMHMMWelcome to CBS http://www.cbs.dtu.dk/index.shtml CBS Prediction Servers http://www.cbs.dtu.dk/services/ TMHMM /protparam/输入FASTA格式序列结果Data 部分数据# WEBSEQUENCE# AA inside membr outside 1 A 0.00271 0.00000 0.99729 2 T 0.00267 0.00004 0.99729 3 G 0.00265 0.00006 0.99729 4 A 0.00265 0.00008 0.99727 5 A 0.00252 0.00022 0.99726 6 A 0.00252 0.00023 0.99726 7 C0.001720.001020.997268 T 0.001720.001020.99726………… ………… 1403 C 0.00059 0.00002 0.99939 1404 G 0.00059 0.00002 0.99939 1405 C 0.00059 0.00002 0.99939 1406 G 0.00059 0.00002 0.99939 1407 A0.000590.000020.999391408 G 0.00059 0.00002 0.99939 1409 A 0.00059 0.00002 0.99939 1410 C 0.00059 0.00002 0.99939 1411 C 0.00059 0.00002 0.99938 1412 T 0.00060 0.00005 0.99935 1413 G 0.00060 0.00009 0.99932 1414 A 0.00060 0.00012 0.99928 1415 A 0.00060 0.00014 0.99926 1416 T 0.00060 0.00016 0.99924 1417 T 0.00060 0.00018 0.99922 1418 G 0.00060 0.00019 0.9992 1419 T 0.00060 0.00023 0.99917 1420 G 0.00060 0.00023 0.99917 1421 T 0.00060 0.00023 0.99918 1422 T 0.00060 0.00023 0.99918 1423 G 0.00059 0.00024 0.99917 1424 C 0.00059 0.00024 0.99917 1425 C 0.00059 0.00024 0.99917 1426 A 0.00059 0.00024 0.99917 1427 G 0.00059 0.00024 0.99917 1428 C 0.00060 0.00024 0.99917 1429 G 0.00060 0.00024 0.99917 1430 G 0.00060 0.00024 0.99917 1431 G 0.00060 0.00023 0.99917 1432 G 0.00060 0.00023 0.99917 1433 A 0.00061 0.00023 0.99917 1434 C 0.00062 0.00021 0.99917 1435 C 0.00066 0.00017 0.99917 1436 T 0.00070 0.00013 0.99917 1437 G 0.00072 0.00011 0.99917 1438 T 0.00075 0.00009 0.99917 1439 G 0.00076 0.00008 0.99917 1440 T 0.00078 0.00006 0.99917 1441 G 0.00079 0.00004 0.99917 1442 T 0.00082 0.00001 0.99917 1443 C 0.00082 0.00001 0.99917 1444 T 0.00082 0.00001 0.99917 1445 G 0.00083 0.00000 0.99917 1446 A 0.00083 0.00000 0.9991712、信号肽及亚细胞定位进入SignalP 4.1 Server http://www.cbs.dtu.dk/services/SignalP/输入FASTA格式序列结果：亚细胞定位： 进入：TargetP 1.1 Server http://www.cbs.dtu.dk/services/TargetP/ 输入序列提交：结果：13、功能分析1）基于序列同源性分析的蛋白质功能预测NCBI----blast 找到吻合相对高的序列查看详情序列同源性蛋白质功能分析NCBI---GENE进入相关文献了解功能2）基于motif、结构位点、结构功能域数据库的蛋白质功能预测Motif:PROSITE//cgi-bin/prosite/ScanView.cgi?scanfile=806498321699.scan.gz结构域基序My Hits:http://hits.isb-sib.ch/cgi-bin/PFSCAN 输入序列结果：http://smart.embl-heidelberg.de/二、蛋白质二级结构预测1）NetTurnP - Prediction of Beta-turns in proteinsNetTurnP 1.0 - Prediction of Beta-turn regions in protein sequenceshttp://www.cbs.dtu.dk/services/NetTurnP/输入序列结果：NetTurnP - Prediction of Beta-turns in proteinsTechnical University of Denmark# For publication of results, please cite:# NetTurnP - Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features.# Petersen B, Lundegaard C, Petersen TN (2010)# PLoS ONE 5(11):e15079 doi:10.1371/journal.pone.0015079## Column 1: Amino acid# Column 2: Sequence name# Column 3: Amino acid number# Column 4: Prediction for Beta-turn# Column 5: Class assignment - "T" for Beta-turn#V Sequence 1 0.287 .T Sequence 2 0.363 .A Sequence 3 0.403 .S Sequence 4 0.482 .E Sequence 5 0.495 .W Sequence 6 0.493 .G Sequence 7 0.552 TP Sequence 8 0.527 TS Sequence 9 0.564 TA Sequence 10 0.572 TD Sequence 11 0.643 TE Sequence 12 0.631 TD Sequence 13 0.620 TQ Sequence 14 0.612 TR Sequence 15 0.497 .S Sequence 16 0.518 TE Sequence 17 0.515 TM Sequence 18 0.557 TK Sequence 19 0.582 TR Sequence 20 0.555 TG Sequence 21 0.561 TM Sequence 22 0.552 TS Sequence 23 0.559 TR Sequence 24 0.560 TG Sequence 25 0.533 TC Sequence 26 0.486 .L Sequence 32 0.179 . M Sequence 33 0.184 .A Sequence 34 0.210 . T Sequence 35 0.236 . V Sequence 36 0.269 . L Sequence 37 0.319 . T Sequence 38 0.396 . V Sequence 39 0.448 . T Sequence 40 0.475 .G Sequence 41 0.505 T A Sequence 42 0.480 . V Sequence 43 0.449 . P Sequence 44 0.455 . V Sequence 45 0.463 . T Sequence 46 0.456 . R Sequence 47 0.467 . P Sequence 48 0.523 T P Sequence 49 0.504 T R Sequence 50 0.492 .A Sequence 51 0.488 . L Sequence 52 0.526 T P Sequence 53 0.568 T D Sequence 54 0.612 T A Sequence 55 0.650 T R Sequence 56 0.585 T G Sequence 57 0.497 .C Sequence 58 0.452 .H Sequence 59 0.380 .I Sequence 60 0.425 .A Sequence 61 0.452 . Q Sequence 62 0.457 .F Sequence 63 0.558 T K Sequence 64 0.524 T S Sequence 65 0.494 . L Sequence 66 0.482 . S Sequence 67 0.347 . P Sequence 68 0.280 . Q Sequence 69 0.259 .E Sequence 70 0.254 . L Sequence 71 0.181 . Q Sequence 72 0.153 .A Sequence 73 0.152 .F Sequence 74 0.167 . K Sequence 75 0.187 .L Sequence 81 0.362 .E Sequence 82 0.382 .E Sequence 83 0.373 . S Sequence 84 0.401 . L Sequence 85 0.373 . L Sequence 86 0.414 . L Sequence 87 0.555 T K Sequence 88 0.547 T D Sequence 89 0.559 T C Sequence 90 0.576 T R Sequence 91 0.414 .C Sequence 92 0.424 . R Sequence 93 0.443 . S Sequence 94 0.442 . R Sequence 95 0.522 T L Sequence 96 0.531 T F Sequence 97 0.572 T P Sequence 98 0.632 T R Sequence 99 0.596 T T Sequence 100 0.572 T W Sequence 101 0.535 TD Sequence 102 0.394 . L Sequence 103 0.416 . R Sequence 104 0.404 . Q Sequence 105 0.398 . L Sequence 106 0.414 . Q Sequence 107 0.371 . V Sequence 108 0.453 . R Sequence 109 0.475 .E Sequence 110 0.472 . R Sequence 111 0.481 . P Sequence 112 0.371 . V Sequence 113 0.271 .A Sequence 114 0.240 . L Sequence 115 0.188 .E Sequence 116 0.182 .A Sequence 117 0.175 .E Sequence 118 0.164 . L Sequence 119 0.168 .A Sequence 120 0.150 . L Sequence 121 0.141 . T Sequence 122 0.142 . L Sequence 123 0.143 .E Sequence 124 0.151 .A Sequence 130 0.479 .D Sequence 131 0.576 T N Sequence 132 0.572 T D Sequence 133 0.541 T M Sequence 134 0.512 T A Sequence 135 0.329 . L Sequence 136 0.275 .G Sequence 137 0.255 .D Sequence 138 0.253 . V Sequence 139 0.278 . L Sequence 140 0.373 .D Sequence 141 0.400 . R Sequence 142 0.395 . P Sequence 143 0.383 . L Sequence 144 0.308 .H Sequence 145 0.244 . T Sequence 146 0.202 . L Sequence 147 0.173 .H Sequence 148 0.152 .H Sequence 149 0.151 . V Sequence 150 0.149 . L Sequence 151 0.152 . S Sequence 152 0.162 . Q Sequence 153 0.173 . L Sequence 154 0.233 . R Sequence 155 0.280 .A Sequence 156 0.306 .C Sequence 157 0.354 . V Sequence 158 0.366 . Q Sequence 159 0.405 . P Sequence 160 0.406 . Q Sequence 161 0.403 . P Sequence 162 0.466 . T Sequence 163 0.517 T A Sequence 164 0.541 T G Sequence 165 0.588 T P Sequence 166 0.540 T R Sequence 167 0.493 . P Sequence 168 0.503 T W Sequence 169 0.433 .G Sequence 170 0.397 . R Sequence 171 0.341 . L Sequence 172 0.232 .H Sequence 173 0.198 .L Sequence 179 0.253 . Q Sequence 180 0.273 .E Sequence 181 0.290 .A Sequence 182 0.447 . P Sequence 183 0.494 . K Sequence 184 0.517 T K Sequence 185 0.554 T E Sequence 186 0.472 . S Sequence 187 0.628 T S Sequence 188 0.604 T G Sequence 189 0.595 T C Sequence 190 0.593 T L Sequence 191 0.334 .E Sequence 192 0.306 .A Sequence 193 0.286 . S Sequence 194 0.243 . V Sequence 195 0.230 . T Sequence 196 0.194 .F Sequence 197 0.177 . N Sequence 198 0.185 . L Sequence 199 0.180 .F Sequence 200 0.181 . R Sequence 201 0.199 . L Sequence 202 0.191 . L Sequence 203 0.249 . T Sequence 204 0.462 . R Sequence 205 0.469 .D Sequence 206 0.466 . L Sequence 207 0.491 . K Sequence 208 0.304 .C Sequence 209 0.311 . V Sequence 210 0.393 .A Sequence 211 0.467 . S Sequence 212 0.554 T G Sequence 213 0.630 T D Sequence 214 0.634 T L Sequence 215 0.593 T C Sequence 216 0.566 T A Sequence 217 0.554 T P Sequence 218 0.579 T S Sequence 219 0.573 T H Sequence 220 0.577 T L Sequence 221 0.544 T P Sequence 222 0.483 .I Sequence 228 0.362 .D Sequence 229 0.326 .F Sequence 230 0.303 .I Sequence 231 0.312 .Y Sequence 232 0.343 .T Sequence 233 0.420 .S Sequence 234 0.480 .T Sequence 235 0.499 .T Sequence 236 0.491 .C Sequence 237 0.509 TL Sequence 238 0.459 .N Sequence 239 0.472 .L Sequence 240 0.475 .L Sequence 241 0.412 .P Sequence 242 0.594 TP Sequence 243 0.599 TN Sequence 244 0.612 TR Sequence 245 0.650 TY Sequence 246 0.368 .Explain the output. Go back.2）GOR - Garnier et al, 1996NPS@ : GOR4 secondary structure predictionhttps://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html结果：3）NetSurfP-1.1 - Protein secondary structure and surface accessibility server http://www.cbs.dtu.dk/services/NetSurfP/结果:NetSurfP - Protein Surface Accessibility andSecondary Structure PredictionsTechnical University of Denmark# For publication of results, please cite:# A generic method for assignment of reliability scores applied to solvent accessibility predictions.# Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen and Claus Lundegaard# BMC Structural Biology 2009, 9:51 doi:10.1186/1472-6807-9-51## Column 1: Class assignment - B for buried or E for Exposed - Threshold: 25% exposure, but not based on RSA# Column 2: Amino acid# Column 3: Sequence name# Column 4: Amino acid number# Column 5: Relative Surface Accessibility - RSA# Column 6: Absolute Surface Accessibility# Column 7: Z-fit score for RSA prediction# Column 8: Probability for Alpha-Helix# Column 9: Probability for Beta-strand# Column 10: Probability for CoilE A Sequence 3 0.434 47.882 -1.297 0.113 0.087 0.800 E S Sequence 4 0.585 68.527 -0.812 0.113 0.087 0.800 E E Sequence 5 0.613 107.109 0.159 0.113 0.087 0.800 B W Sequence 6 0.249 59.981 -0.639 0.052 0.084 0.864 E G Sequence 7 0.338 26.577 -0.814 0.053 0.043 0.903 E P Sequence 8 0.410 58.207 -1.117 0.053 0.043 0.903 E S Sequence 9 0.584 68.410 -1.020 0.053 0.043 0.903 E A Sequence 10 0.367 40.388 -1.062 0.058 0.017 0.925 E D Sequence 11 0.536 77.238 -0.648 0.053 0.043 0.903 E E Sequence 12 0.644 112.542 -0.710 0.184 0.043 0.773 E D Sequence 13 0.581 83.708 -1.977 0.184 0.043 0.773 E Q Sequence 14 0.508 90.693 -0.589 0.268 0.043 0.689 E R Sequence 15 0.464 106.302 -0.355 0.354 0.048 0.598 E S Sequence 16 0.414 48.533 -1.835 0.354 0.048 0.598 E E Sequence 17 0.592 103.370 -0.492 0.354 0.048 0.598 E M Sequence 18 0.400 80.020 -1.980 0.354 0.048 0.598 E K Sequence 19 0.526 108.198 -0.605 0.278 0.093 0.628 E R Sequence 20 0.472 108.180 -0.949 0.113 0.087 0.800 B G Sequence 21 0.272 21.391 -2.226 0.113 0.087 0.800 B M Sequence 22 0.197 39.440 -0.962 0.118 0.150 0.732 B S Sequence 23 0.281 32.875 -1.279 0.118 0.150 0.732 E R Sequence 24 0.291 66.593 -1.665 0.191 0.086 0.723 B G Sequence 25 0.158 12.458 -1.360 0.268 0.043 0.689 B C Sequence 26 0.026 3.678 -0.098 0.502 0.102 0.396 B M Sequence 27 0.143 28.634 0.257 0.725 0.163 0.112 B A Sequence 28 0.104 11.483 -0.200 0.725 0.163 0.112 B V Sequence 29 0.048 7.454 0.791 0.807 0.137 0.056 B L Sequence 30 0.041 7.507 0.219 0.870 0.077 0.053 B V Sequence 31 0.081 12.465 -0.059 0.886 0.090 0.024 B L Sequence 32 0.067 12.213 0.544 0.870 0.077 0.053 B M Sequence 33 0.073 14.667 0.432 0.870 0.077 0.053 B A Sequence 34 0.072 7.901 -0.058 0.831 0.044 0.125 B T Sequence 35 0.115 16.020 -0.434 0.831 0.044 0.125 B V Sequence 36 0.128 19.735 -0.312 0.831 0.044 0.125 B L Sequence 37 0.130 23.730 0.063 0.751 0.050 0.199 B T Sequence 38 0.266 36.964 -0.231 0.660 0.049 0.291 E V Sequence 39 0.339 52.104 -1.218 0.354 0.048 0.598 E T Sequence 40 0.409 56.770 -2.017 0.184 0.043 0.773 B G Sequence 41 0.313 24.625 -1.553 0.053 0.043 0.903 E A Sequence 42 0.370 40.752 -2.039 0.018 0.088 0.893 B V Sequence 43 0.186 28.542 -0.494 0.020 0.205 0.775 E P Sequence 44 0.337 47.806 -1.325 0.020 0.205 0.775 B V Sequence 45 0.170 26.206 -1.051 0.018 0.088 0.893 E T Sequence 46 0.381 52.803 -1.502 0.018 0.047 0.935 E R Sequence 47 0.526 120.362 -0.292 0.018 0.019 0.964 B P Sequence 48 0.241 34.127 -1.181 0.018 0.019 0.964 E P Sequence 49 0.395 56.079 -1.454 0.018 0.019 0.964E L Sequence 52 0.335 61.265 -0.180 0.018 0.047 0.935 E P Sequence 53 0.340 48.232 -0.691 0.018 0.047 0.935 E D Sequence 54 0.732 105.424 0.275 0.018 0.019 0.964 E A Sequence 55 0.475 52.301 -1.315 0.018 0.019 0.964 E R Sequence 56 0.514 117.660 -0.150 0.018 0.047 0.935 E G Sequence 57 0.466 36.698 -0.497 0.019 0.141 0.840 B C Sequence 58 0.061 8.578 -0.417 0.021 0.279 0.699 E H Sequence 59 0.342 62.283 0.151 0.022 0.359 0.619 B I Sequence 60 0.110 20.368 -0.560 0.022 0.359 0.619 E A Sequence 61 0.325 35.848 -1.172 0.020 0.205 0.775 E Q Sequence 62 0.503 89.872 0.409 0.019 0.141 0.840 BF Sequence 63 0.126 25.348 -0.199 0.018 0.088 0.893 E K Sequence 64 0.564 116.077 0.135 0.018 0.088 0.893 E S Sequence 65 0.482 56.444 -1.479 0.018 0.047 0.935 B L Sequence 66 0.207 37.902 -0.776 0.018 0.019 0.964 E S Sequence 67 0.392 45.966 0.122 0.018 0.019 0.964 E P Sequence 68 0.386 54.802 -1.124 0.858 0.002 0.139 E Q Sequence 69 0.509 90.872 -0.427 0.923 0.002 0.076 B E Sequence 70 0.213 37.159 -0.370 0.923 0.002 0.076 B L Sequence 71 0.196 35.961 0.420 0.970 0.001 0.030 E Q Sequence 72 0.476 84.960 0.319 0.970 0.001 0.030 B A Sequence 73 0.118 13.048 -0.154 0.970 0.001 0.030 B F Sequence 74 0.061 12.263 0.168 0.970 0.001 0.030 E K Sequence 75 0.402 82.630 1.003 0.923 0.002 0.076 E R Sequence 76 0.407 93.249 1.034 0.923 0.002 0.076 B A Sequence 77 0.046 5.047 0.102 0.858 0.002 0.139 E K Sequence 78 0.339 69.732 0.957 0.858 0.002 0.139 E D Sequence 79 0.535 77.122 0.100 0.858 0.002 0.139 B A Sequence 80 0.222 24.497 0.325 0.858 0.002 0.139 B L Sequence 81 0.086 15.783 0.088 0.802 0.014 0.185 E E Sequence 82 0.421 73.479 0.113 0.802 0.014 0.185 E E Sequence 83 0.579 101.064 -0.635 0.717 0.014 0.269 B S Sequence 84 0.234 27.437 -1.170 0.622 0.015 0.363 B L Sequence 85 0.140 25.726 -0.141 0.522 0.016 0.462 B L Sequence 86 0.258 47.203 -0.156 0.455 0.046 0.498 B L Sequence 87 0.251 45.976 -0.887 0.268 0.043 0.689 E K Sequence 88 0.591 121.651 -0.038 0.191 0.086 0.723 E D Sequence 89 0.577 83.160 -0.834 0.052 0.084 0.864 B C Sequence 90 0.214 29.989 0.573 0.056 0.142 0.802 E R Sequence 91 0.462 105.752 0.703 0.066 0.296 0.638 B C Sequence 92 0.092 12.945 -0.868 0.066 0.296 0.638 E R Sequence 93 0.441 100.897 -0.588 0.064 0.216 0.721 E S Sequence 94 0.347 40.668 -1.463 0.019 0.141 0.840 E R Sequence 95 0.456 104.538 -0.134 0.020 0.205 0.775 B L Sequence 96 0.213 39.055 -1.115 0.021 0.279 0.699 B F Sequence 97 0.137 27.576 0.398 0.019 0.141 0.840 E P Sequence 98 0.373 52.957 -0.918 0.018 0.088 0.893B W Sequence 101 0.197 47.354 0.333 0.125 0.227 0.648 E D Sequence 102 0.408 58.850 0.628 0.125 0.227 0.648 B L Sequence 103 0.135 24.664 0.252 0.216 0.235 0.548 E R Sequence 104 0.493 112.989 0.612 0.216 0.235 0.548 E Q Sequence 105 0.460 82.102 0.772 0.321 0.252 0.427 B L Sequence 106 0.109 19.995 0.672 0.216 0.235 0.548 E Q Sequence 107 0.423 75.548 0.333 0.199 0.152 0.649 B V Sequence 108 0.126 19.428 0.026 0.307 0.165 0.527 E R Sequence 109 0.384 88.005 0.285 0.278 0.093 0.628 E E Sequence 110 0.570 99.527 -0.787 0.354 0.048 0.598 B R Sequence 111 0.242 55.487 0.547 0.561 0.047 0.393 B P Sequence 112 0.212 30.111 -0.237 0.717 0.014 0.269 E V Sequence 113 0.264 40.608 0.527 0.831 0.044 0.125 B A Sequence 114 0.129 14.216 -0.416 0.911 0.033 0.057 B L Sequence 115 0.071 13.073 0.588 0.911 0.033 0.057 E E Sequence 116 0.312 54.576 0.365 0.938 0.007 0.055 B A Sequence 117 0.118 12.982 -0.203 0.938 0.007 0.055 B E Sequence 118 0.226 39.395 0.183 0.911 0.033 0.057 B L Sequence 119 0.058 10.638 0.730 0.911 0.033 0.057 E A Sequence 120 0.387 42.614 0.935 0.911 0.033 0.057 B L Sequence 121 0.109 20.013 0.598 0.831 0.044 0.125 B T Sequence 122 0.078 10.846 0.183 0.918 0.063 0.019 B L Sequence 123 0.077 14.117 0.561 0.911 0.033 0.057 E E Sequence 124 0.439 76.623 1.894 0.950 0.028 0.022 B V Sequence 125 0.081 12.388 0.564 0.950 0.028 0.022 B L Sequence 126 0.069 12.579 0.437 0.879 0.010 0.111 E E Sequence 127 0.476 83.210 0.447 0.879 0.010 0.111 E A Sequence 128 0.489 53.833 -0.563 0.622 0.015 0.363 B T Sequence 129 0.204 28.281 -0.526 0.339 0.016 0.645 E A Sequence 130 0.424 46.714 -0.865 0.109 0.005 0.886 E D Sequence 131 0.581 83.664 0.009 0.053 0.005 0.942 E N Sequence 132 0.499 73.112 -1.368 0.053 0.005 0.942 E D Sequence 133 0.550 79.255 -1.082 0.176 0.004 0.820 E M Sequence 134 0.529 105.773 0.296 0.502 0.002 0.495 E A Sequence 135 0.313 34.548 0.985 0.802 0.014 0.185 B L Sequence 136 0.053 9.778 0.183 0.923 0.002 0.076 B G Sequence 137 0.212 16.669 -0.022 0.970 0.001 0.030 E D Sequence 138 0.544 78.390 0.415 0.970 0.001 0.030 B V Sequence 139 0.096 14.755 0.975 0.938 0.007 0.055 B L Sequence 140 0.041 7.489 0.162 0.879 0.010 0.111 E D Sequence 141 0.490 70.609 0.135 0.600 0.003 0.397 E R Sequence 142 0.403 92.241 0.602 0.502 0.002 0.495 B P Sequence 143 0.092 12.984 0.209 0.600 0.003 0.397 B L Sequence 144 0.084 15.325 0.131 0.782 0.003 0.216 E H Sequence 145 0.361 65.630 -0.192 0.923 0.002 0.076 B T Sequence 146 0.132 18.336 -0.058 0.923 0.002 0.076 B L Sequence 147 0.038 6.958 0.485 0.970 0.001 0.030 E H Sequence 148 0.348 63.247 0.498 0.970 0.001 0.030 E H Sequence 149 0.331 60.136 0.839 0.970 0.001 0.030B V Sequence 150 0.041 6.348 0.473 0.970 0.001 0.030 B L Sequence 151 0.173 31.676 0.458 0.970 0.001 0.030 E S Sequence 152 0.550 64.472 0.552 0.970 0.001 0.030 B Q Sequence 153 0.280 49.954 0.494 0.970 0.001 0.030 B L Sequence 154 0.060 11.023 0.197 0.923 0.002 0.076 E R Sequence 155 0.443 101.378 1.090 0.858 0.002 0.139 E A Sequence 156 0.519 57.216 0.794 0.694 0.003 0.303 BC Sequence 157 0.076 10.727 -0.397 0.600 0.003 0.397 B V Sequence 158 0.214 32.846 -0.023 0.430 0.016 0.555 E Q Sequence 159 0.581 103.749 0.558 0.181 0.016 0.803 E P Sequence 160 0.372 52.815 -0.699 0.053 0.043 0.903 E Q Sequence 161 0.518 92.479 -0.120 0.018 0.019 0.964 B P Sequence 162 0.229 32.552 -1.009 0.018 0.019 0.964 E T Sequence 163 0.558 77.381 -0.839 0.018 0.019 0.964 E A Sequence 164 0.573 63.101 -1.965 0.018 0.019 0.964 E G Sequence 165 0.501 39.429 -1.447 0.018 0.019 0.964 E P Sequence 166 0.502 71.234 -1.690 0.018 0.019 0.964 E R Sequence 167 0.404 92.424 -0.216 0.018 0.047 0.935 B P Sequence 168 0.281 39.916 -1.411 0.115 0.016 0.868 E W Sequence 169 0.443 106.638 -0.546 0.339 0.016 0.645 E G Sequence 170 0.290 22.847 -2.131 0.522 0.016 0.462 B R Sequence 171 0.219 50.128 0.487 0.802 0.014 0.185 B L Sequence 172 0.041 7.562 -0.568 0.938 0.007 0.055 E H Sequence 173 0.310 56.334 0.581 0.923 0.002 0.076 E H Sequence 174 0.347 63.156 0.424 0.970 0.001 0.030 B W Sequence 175 0.066 15.753 0.456 0.970 0.001 0.030 B L Sequence 176 0.068 12.414 0.160 0.970 0.001 0.030 E H Sequence 177 0.394 71.760 0.246 0.970 0.001 0.030 E R Sequence 178 0.303 69.364 1.450 0.923 0.002 0.076 B L Sequence 179 0.055 10.052 0.711 0.858 0.002 0.139 E Q Sequence 180 0.443 79.120 0.982 0.782 0.003 0.216 E E Sequence 181 0.620 108.314 1.492 0.600 0.003 0.397 B A Sequence 182 0.100 10.998 -0.174 0.176 0.004 0.820 E P Sequence 183 0.519 73.618 0.665 0.109 0.005 0.886 E K Sequence 184 0.729 149.894 0.904 0.181 0.016 0.803 E K Sequence 185 0.619 127.267 0.262 0.115 0.016 0.868 E E Sequence 186 0.510 89.062 -0.518 0.115 0.016 0.868 E S Sequence 187 0.407 47.689 -0.749 0.115 0.016 0.868 E S Sequence 188 0.454 53.185 -0.258 0.257 0.016 0.727 E G Sequence 189 0.289 22.744 -0.967 0.354 0.048 0.598 B C Sequence 190 0.064 9.014 -0.312 0.502 0.102 0.396 B L Sequence 191 0.115 21.075 -0.202 0.649 0.163 0.188 E E Sequence 192 0.325 56.830 0.201 0.701 0.107 0.192 B A Sequence 193 0.086 9.488 -0.828 0.779 0.100 0.120 B S Sequence 194 0.136 15.927 0.029 0.779 0.100 0.120 B V Sequence 195 0.065 9.914 -0.429 0.779 0.100 0.120 B T Sequence 196 0.085 11.817 -0.319 0.870 0.077 0.053 B F Sequence 197 0.072 14.511 0.097 0.911 0.033 0.057 B N Sequence 198 0.150 21.989 -0.346 0.879 0.010 0.111B L Sequence 199 0.057 10.492 0.062 0.938 0.007 0.055B F Sequence 200 0.081 16.176 0.103 0.938 0.007 0.055E R Sequence 201 0.258 59.013 1.046 0.938 0.007 0.055B L Sequence 202 0.082 14.959 0.208 0.879 0.010 0.111B L Sequence 203 0.067 12.249 0.337 0.879 0.010 0.111B T Sequence 204 0.240 33.343 0.112 0.717 0.014 0.269E R Sequence 205 0.489 112.050 0.481 0.430 0.016 0.555E D Sequence 206 0.433 62.366 -0.416 0.257 0.016 0.727B L Sequence 207 0.084 15.399 0.517 0.191 0.086 0.723E K Sequence 208 0.501 103.159 1.207 0.231 0.330 0.439B C Sequence 209 0.097 13.675 0.387 0.268 0.505 0.227B V Sequence 210 0.137 21.057 0.261 0.268 0.505 0.227B A Sequence 211 0.306 33.699 -0.976 0.135 0.317 0.548E S Sequence 212 0.529 61.987 -0.462 0.056 0.142 0.802E G Sequence 213 0.427 33.636 -1.328 0.018 0.047 0.935E D Sequence 214 0.636 91.705 -1.310 0.018 0.047 0.935B L Sequence 215 0.288 52.660 -0.493 0.052 0.084 0.864B C Sequence 216 0.088 12.327 -0.952 0.056 0.142 0.802E A Sequence 217 0.282 31.032 -0.158 0.052 0.084 0.864E P Sequence 218 0.369 52.304 -0.980 0.053 0.043 0.903E S Sequence 219 0.571 66.909 -1.224 0.053 0.043 0.903E H Sequence 220 0.419 76.125 -1.162 0.053 0.043 0.903B L Sequence 221 0.149 27.264 0.307 0.053 0.043 0.903E P Sequence 222 0.336 47.622 -0.813 0.113 0.043 0.844B A Sequence 223 0.295 32.520 -1.323 0.113 0.087 0.800E T Sequence 224 0.276 38.309 -0.522 0.191 0.086 0.723B H Sequence 225 0.267 48.640 -0.426 0.199 0.152 0.649B H Sequence 226 0.283 51.514 -0.300 0.216 0.235 0.548B A Sequence 227 0.115 12.695 -0.606 0.231 0.330 0.439B I Sequence 228 0.062 11.507 0.198 0.252 0.423 0.325B D Sequence 229 0.222 32.033 -0.360 0.252 0.423 0.325B F Sequence 230 0.088 17.762 0.207 0.273 0.587 0.140B I Sequence 231 0.071 13.154 -0.244 0.273 0.587 0.140B Y Sequence 232 0.153 32.717 0.494 0.268 0.505 0.227B T Sequence 233 0.215 29.793 -0.735 0.252 0.423 0.325B S Sequence 234 0.254 29.804 -1.090 0.216 0.235 0.548B T Sequence 235 0.277 38.475 -0.682 0.307 0.165 0.527B T Sequence 236 0.258 35.785 -0.222 0.199 0.152 0.649B C Sequence 237 0.072 10.067 -0.863 0.216 0.235 0.548B L Sequence 238 0.158 28.875 -0.255 0.216 0.235 0.548E N Sequence 239 0.462 67.564 -0.902 0.216 0.235 0.548B L Sequence 240 0.189 34.661 -0.397 0.113 0.087 0.800B L Sequence 241 0.210 38.451 0.093 0.053 0.043 0.903E P Sequence 242 0.379 53.752 -0.085 0.018 0.019 0.964E P Sequence 243 0.466 66.125 -1.303 0.018 0.019 0.964E N Sequence 244 0.670 98.132 -2.145 0.018 0.047 0.935E R Sequence 245 0.568 130.095 -0.533 0.018 0.019 0.964E Y Sequence 246 0.734 156.941 -1.908 0.003 0.003 0.994Explain the output. Go back.5）PORTERhttp://distill.ucd.ie/porter/结果：Subject: Porter response toQuery_name:Query_length: 248Prediction: VTASEWGPSADEDQRSEMKRGMSRGCMAVLVLMATVLTVTGAVPVTRPPRALPDARGCHICCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHAQFKSLSPQELQAFKRAKDALEESLLLKDCRCRSRLFPRTWDLRQLQVRERPVALEAELA HHHCCCCHHHHHHHHHHHHHHHHHHCECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHLTLEVLEATADNDMALGDVLDRPLHTLHHVLSQLRACVQPQPTAGPRPWGRLHHWLHRLQ HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCEAPKKESSGCLEASVTFNLFRLLTRDLKCVASGDLCAXPSHLPATHHAIXDFIYTSTTCL CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCHHHNLLPPNRYCCCCCCCCPredictions based on PDB templates (seq. similarity up to 58.5%)Query served in 59 secondsMultiple queries to multiple servers at:http://distill.ucd.ie/distill/Access individually Porter, Porter+, PaleAle, BrownAle, X-Stout , XX-Stout, 3Distill at: http://distill.ucd.ie/porter/http://distill.ucd.ie/porter+/http://distill.ucd.ie/paleale/http://distill.ucd.ie/brownale/http://distill.ucd.ie/xstout/http://distill.ucd.ie/xxstout/Prediction of protein disorder by Spritz:http://distill.ucd.ie/spritz/For an explanation of the output formats, refer to:http://distill.ucd.ie/distill/explanation.html#output_formats Please cite one or more of the following:G.Pollastri, A.McLysaght."Porter: a new, accurate server for protein secondary structure prediction". Bioinformatics, 21(8):1719-1720, 2005./cgi/content/abstract/21/8/1719C.Mooney, Y.Wang, G.Pollastri."SCLpred: Protein Subcellular Localization Prediction by N-to-1 Neural Networks", Bioinformatics, 27 (20), 2812-2819, 2011./content/27/20/2812D.Bau, A.J.M.Martin, C.Mooney, A.Vullo, I.Walsh, G.Pollastri. "Distill: Asuite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins" BMC Bioinformatics, 7:402, 2006./1471-2105/7/402/abstractC. Mooney, G.Pollastri "Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information" Proteins, 77(1), 181-90, 2009. /journal/122274852/abstract G.Pollastri, A.J.M.Martin, C.Mooney, A.Vullo. "Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information" BMC Bioinformatics, 8:201, 2007. /1471-2105/8/201/abstract I.Walsh,D.Bau, .M.Martin, C. Mooney, A.Vullo, G.Pollastri "Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks" BMC Structural Biology, 9:5, 2009. /1472-6807/9/5A.Vullo, I.Walsh, G.Pollastri."A two-stage approach for improved prediction of residue contact maps"BMC Bioinformatics, 7:180, 2006. /1471-2105/7/180/abstractG. Pollastri, A. Vullo, P . Frasconi, P . Baldi."Modular DAG-RNN Architectures for Assembling Coarse Protein Structures".Journal of Computational Biology, 13:3, 631-650, 2006.A. Vullo, O. Bortolami, G. Pollastri, S. Tosatto."Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines"Nucleic Acids Research, 34:W164-W168, 2006. 6）TUAT Kuroda Lab's Programb.tuat.ac.jp/dlpsvm.html结果：部分数据Sequence position Prob. by SVM-ALL Prob. by SVM-Long Prob. by SVM-Short Li 1 0 A2 0 T3 0 G4 0 A5 -0.973539 0 0 A6 -1.086915 0 0 A7 -0.891253 0 0 C8 -0.644379 0 0 T9 -0.378074 0 0 A。

蛋白质数据库及其结构预测攻略一、蛋白质结构层次一般情况下，蛋白质的结构分为4 个层次：▪初级结构——氨基酸序列；▪二级结构——а螺旋(alpha-helix)，β折叠(β-sheets)，β转角，无规则卷曲（random coil）▪三级结构——三维结构，由模体（motif）和结构域（domain）组成；▪四级结构——亚基之间的互作。

二、蛋白质数据库：1. 蛋白质一级数据库1.1序列数据库：UniProt包含三大蛋白质序列数据库，Swiss-Prot，TrEMBL 和PIR，分为三个层次：第一层叫UniParc，收录了所有UniProt 数据库子库中的蛋白质序列，量大，粗糙。

第二层是UniRef，他归纳了UniProt 几个主要数据库并且是将重复序列去除后的数据库。

第三层是UniProtKB，他有详细注释并与其他数据库有链接，分为Swiss-Prot（最有用的）和TrEMBL。

1.2蛋白质结构数据库PDBPDB存储生物大分子3D 结构。

这些生物大分子除了蛋白质以外还包括核酸以及核酸和蛋白质的复合物。

只有通过实验方法获得的3D 结构才会被收入其中。

PDB文件是一堆数字字母，那是每个原子的坐标，一般用用可视化软件VMD打开，免费的，这里不作具体说明。

2. 蛋白质二级数据库2.1结构域家族Pfam数据库Pfam 主页上的搜索工具可以查找某条序列上有哪些结构域。

2.2结构分类数据库CATHCATH是四种结构分类层次的首字母。

根据PDB编号搜索，可以获得各层次具体的结构分类信息以及各种结构相关分析信息、聚类分析。

2.3结构分类数据库SCOP2在搜集、整理、分析PDB数据中已知的蛋白质三维结构的基础上，详细描述了一直结构的蛋白质在结构、进化事件与功能类型三个方面的关系，主要依赖人工验证。

三、蛋白质结构研究1.二级结构1.1已知PDB-输入检索号-sequence- view sequence& DSSP image1.2未知预测网址如下：输入氨基酸序列，等待大概半小时。