swiss-model的使用

《生物信息学》第五章：蛋白质结构预测与分析（第二部分） 计算方法预测三级结构：同源建模法SWISS-MODEL预测蛋白质三级结构的首选方法是同源建模法（homolog modeling）。

该方法基于原理：相似的氨基酸序列对应着相似的蛋白质结构。

比如三个蛋白质，它们在序列水平上十分相似，解析出的结构也十分相似。

第四个蛋白质的序列和前面三个也高度相似，那么就可以比着前三个结构的样子“画”出第四个的样子。

所以同源建模法的关键就是找到一个好的模板。

好的模板要求，在序列水平上模板（template）要与目标（target）蛋白质具有超过30%的一致度。

同源建模法操作流程如下（图1）：图1. 同源建模法操作流程1. 确定模板：找到与目标蛋白质同源的已知蛋白质结构作为模版（目标序列与模版序列间的一致度要≥30%）。

2. 序列比对：为目标序列与模板序列创建序列对比。

模板可以选取多个，通过做多序列比对，各取所长，让模板序列中与目标序列相似的片段尽可能多的覆盖整个目标序列，同时要尽量避免没有模板参考的断口。

3. 计算模型：通过序列比对，将目标序列里的氨基酸替换到模板结构里对应的氨基酸所在的空间位置上。

这一步通过同源建模软件来实现。

4.换模板或修正序列比对，重新构建模型，再次评估。

SWISS-MODEL（）它能帮助完成上述步骤中从模板选取到创建序列比对，再到计算模型，以及最后的质量评估的全部过程。

你需要做的只是：输入目标序列，点Build Model（创建模型）（图2左）。

大约三到五分钟之后就会返回结果。

如果这种自动挡模式不能满足你的要求，可以通过点击Search For Templates切换成手动挡，以便指定模板。

也可以直接把做好的目标序列与模板序列之间的序列比对按照指定格式黏贴到输入框里，再点击Build Model（创建模型）（图2右）。

这时，SWISS-MODEL会根据输入的特定格式的序列比对，识别出哪个是目标序列，哪个是模板，并自动从PDB数据库下载模板结构，最后根据输入的比对计算结构模型。

Trigo Product CenterRelease Notes Fix pack 4.1.0.13aNote: Before using this information and the product it supports, read the information in “Notices”at the end of this document.10 June 2006This edition of this document applies to Trigo Product Center, version 4.1.0.13a, and to all subsequent releases and modifications until otherwise indicated in new editions.© Copyright International Business Machines Corporations 2006. All rights reserved. Licensed Materials-Property of IBM. US Government Users Restricted Rights – Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp.Table of Contents1. Overview (2)1.1 Fix pack requirements (2)2. Product fixes (2)2.1 Fixes for 4.1.0.13a (2)2.2 Fixes for 4.1.0.12a (2)2.3 Fixes for 4.1.0.11 (3)2.3.1Override with Blank feature disabled (3)2.4 Fixes for 4.1.0.10 (3)2.5 Fixes for 4.1.0.9 (3)2.6 Fixes for 4.1.0.8a (4)2.7 Fixes for 4.1.0.8 (4)2.8 Fixes for 4.1.0.7 (5)3. Known issues and limitations (5)4. Installation (5)4.1 Installation notes (5)4.1.1Removal of J2EE and JSSE (5)4.2 Preparation (7)4.2.1Stopping the whole application on the local machine (7)4.2.2Backup (7)4.2.3Delete Tomcat working directory (8)4.3 Apply Fix Pack (8)4.3.1Unpack tar file (8)4.3.2Verify configuration files (8)4.4 Test installation (9)4.4.1Start Trigo Product Center (9)4.4.2Check status (10)1. OverviewThis document addresses customer requests, installation instructions, and notes for Trigo Product Center Fix Pack 4.1.0.13a on the following platform:•Tomcat/Oracle1.1 Fix pack requirementsTrigo Product Center 4.1.0.7 must be installed prior to the application of Fix Pack 4.1.0.13a. Ifworking with a version prior to 4.1.0.7, it is required to upgrade to 4.1.0.7 first and then apply the4.1.0.13a Fix Pack.2. Product fixesThis section identifies issues that have been reported and resolved with the application of this fix pack.Note: The Tracking Number column uses APAR, PMR, and Internal CR record numbers.2.1 Fixes for 4.1.0.13aDescriptionTrackingNumberJR23783 Cannot import all items from a cvs file.2.2 Fixes for 4.1.0.12aDescriptionTrackingNumberJR22156 Cannot delete spec, even if not in useJR21730 Attribute Search choice should jump.Impact: No change in the UI. Grouped attributes are highlighted when searched forin tab view.JR22158 Empty paths displayed in left paneJR22547 Jobs failing after MTPing 4.1.0.10 in production2.3 Fixes for 4.1.0.11DescriptionTrackingNumberJR21938 Attribute not included in exportJR21924 Attribute order changing from sub-spec to secondary specJR21688 Inheritance path and source not displayedJR22037 Inheritance Rules lost when category tree is rolled backJR21470 Category search unsuccessful - if category name contains "+ "JR22213 IPG Performance comparisonJR22482 Can't override the inherited value through scripting2.3.1 Override with Blank feature disabledProblem: The change made in 4.1.0.9 was for attribute values to be trimmed before being saved.This change was made so that there is proper matching of attribute values (i.e. for lookup tables).However, a problem surfaces when blank spaces are used to override inheritance. The trim fixdisables the overriding feature.Solution: A simple fix will be made to keep the trim fix intact. Trimming is done only forattributes with non-blank characters. Meaning "A " and " A" will be trimmed to "A", but " " will remain as " ".2.4 Fixes for 4.1.0.10TrackingDescriptionNumber18654 Fixes & Optimization of duplicate sub spec script operationsNA Back port of custom export/import tool – Refer to "Export/Import User Guide" for additional information.2.5 Fixes for 4.1.0.9DescriptionTrackingNumberJR21056 Incorrect duplicate sub spec errorJR21036 Script parsing error (explicit final new line required)JR20850 getSpecNameList() does not work for SUB_SPEC parameter valueJR21055 getSpecNameList() returns all spec names for CATEGORY_TREE_SPEC parameter, instead of just the category tree specsJR20852 Get inheritance rule by attribute full path returns no resultJR20981 Lookup table keys don't get leading/trailing white space trimmedJR21123 Fix multi-occurrence ordering on importJR21061 Unexpected results when using the copy toolJR20610 Inheritance source goes to wrong placeJR21469 Issue with non-persistent attributes2.6 Fixes for 4.1.0.8aTrackingNumberDescriptionJR21238 Workflow scheduler stuck on productionDebug code has been added to catch and report certain Java exceptions that willbe thrown if corruptions of workflow static data occur in the database. Forexample, if rows are deleted from the db tables containing workflow static data,while collaboration area that references the workflow still has items movingthrough it. Data corruption should never occur of course; hence these particularJava exceptions should actually never occur.JR21206 Using getFullHTTPResponse(..) method to download zip files.2.7 Fixes for 4.1.0.8Tracking number Description01638Positional placement of new spec attributes.04359Rollback the changeover to the light Data Entry UI screens13524 Ordering of locale attributes is not consistent across specs when new locales are added to the system01114 Clicking on source of inheritance does not direct to the exact location of the attribute15080 Cannot add subspec attribute through spec association screen if Secondary spec or category spec has only single node.15584 View code not handling an invalid attribute properly15634 Extra line ${RM} ${TOP}/etc/tomcat33/webapps/trigo in start_appsvr.sh script removes tomcat working dir15743 Duplicate sub spec validation error preventing save of category entries13405 Redundant execution of queries15761 ItemEdit widget exception when trying to display inherited value2.8 Fixes for 4.1.0.7Refer to the release notes for maintenance releases 4.1.0.7-4.1.0.7c.3. Known issues and limitationsThe following table identifies known issues and limitations related to this release.JR22268 Inconsistent Attribute Values in system-default and user-defined views. Targeted to be addressed for 4.1.0.13JR21545 Issue with displaying inheritance rules. Debug code was implemented in 4.1.0.9 to better analyze the issue and to aid in providing a solution for a future Fix Pack.18633 When removing a subspec, an error occurs stating that a duplicate subspec has been added. The error should not occur as the subspec is removed.Workaround: Log out of WebSphere Product Center and log back in to clear the errormessage.4. InstallationThis section provides general guidelines to apply a Fix Pack to Trigo Product Center. Someinformation may differ depending on the methods used for previous installations. Contact your support representative for Trigo Product Center with any installation issues.4.1 Installation notesPreviously, it was necessary to perform a full installation for all files. The current installationprocess only updates the files that have changed to the current working version directory.4.1.1 Removal of J2EE and JSSECR: P12188Due to new company guidelines, J2EE and JSSE are no longer bundled as part of the Trigoinstallation file. This is not an issue for customers using WebSphere or WebLogic, only customers using Tomcat.J2EE - Java 2 Platform, Enterprise EditionJ2EE is a Trigo prerequisite with the use of Tomcat; therefore the J2EE JAR file, which is part of “Version 1.3.1 of the Java 2 SDK, Enterprise Edition ("J2EE" SDK)”, will need to be downloaded by the customer from the Sun Microsystems website (/j2ee/sdk_1.3/). Follow the instructions on the website to download and install the entire J2EE SDK.Note: The J2EE jar file is included in the J2EE SDK tar file.Figure 1 - Link to download J2EE SDK tar fileOnce this tar file is downloaded, it is extracted to a location defined by the customer.Since j2ee.jar is no longer included when a Trigo enterprise build is created and it is a prerequisite for Trigo Product Center, the following environment variable needs to be set to identify the location of the j2ee.jar file. The environment variable is defined in the init_trigo_vars.sh file.File to edit:$TOP/setup/init_trigo_vars.shEnvironment variable:J2EE_JAR=(location of j2ee.jar file including the file name)For Example:J2EE_JAR=/opt/j2sdkee1.3.1/lib/j2ee.jarNote: This step is not required for WebSphere or WebLogic.JSSE - Java Secure Socket ExtensionJSSE was being used to provide HTTPS post functionality. After careful review, it was determined that this functionality was not being used, therefore the functionality and the associated JAR file were removed.4.2 PreparationBefore attempting to apply the latest Fix Pack to Trigo Product Center, the following preparation is recommended:4.2.1 Stopping the whole application on the local machineComplete the following steps to stop the Trigo Product Center instance:1. Check the scheduler to make sure there are no critical jobs that need to be completed.If the queue is clear, kill the scheduler manually by running the script:$TOP/bin/go/stop/stop_scheduler.sh2. Abort the entire application by running the script:$TOP/bin/go/abort_local.shAll services running on the local machine are aborted. The RMI registry is aborted.Note: Check to make sure all processes have stopped using the 'ps' command.Kill any rogue "java" or "rmiregistry" processes that remain after shutting down the instance.Occasionally, it may take several attempts to kill all java processes.4.2.2 Backup•Create a full backup of the current Trigo Product Center directories before applying the Fix Pack. The Fix Pack will overwrite files that have changed. If any issues occur, thebackup will allow a rollback to a previous version•It is recommended to apply the Fix Pack to a test system to identify any issues before applying the Fix Pack to a production system•Perform a full backup of the database before applying the Fix Pack to a production system Note: Do not delete the old Trigo Product Center version until thorough testing of the new installation is completed.4.2.3 Delete Tomcat working directoryFor configurations using Tomcat, delete the Tomcat working directory using the followingcommand:rm -rf $TOP/etc/default/tomcat33/webapps/ccdOnce the working directory has been deleted, begin the application of the Fix Pack.4.3 Apply Fix PackTo apply the Fix Pack to Trigo Product Center, complete the following tasks:Unpack tar fileUpdate configuration filesTest installation4.3.1 Unpack tar filePurpose: To extract and update any new installation files into the current working directoryNote: GNU tar is needed to untar the Trigo Product Center files.1.Copy the Trigo Product Center tar file to the user or temporary directory.Example:{HOME_OF_TRIGO}/tarballs2. CD to $TOP, the current working directory, and unpack the tar file:Using GNU tar, the following command extracts and unzips the tar file:Example:Tar using an absolute path:tar zxvf /home/trigo/tarballs/trigo_4107a_05_fixpak_tom_ora.tgz 4.3.2 Verify configuration filesVerify all configuration files required by the new installation and make any updates as needed.Refer to the backup copy of the configuration files for the previous installation if needed.austin.propertiesadmin_properties.xmlinit_trigo_vars.shTrigo license fileaustin.propertiesOn startup, the system will use this file to read in all system level parameters. This fileincludes settings for the database layer (connection parameters), directory settings,default character sets, thread-pooling parameters, and other settings, which aredocumented in the file.File location: $TOP/etcadmin_properties.xmlThis file is used by the administrative utilities to configure clusters of the application.File location: $TOP/etcinit_trigo_vars.shThe initialization file is the shell script that initializes the shell variables used by thesystem.File location: $TOP/setupTrigo License FileThe license file contains the license keys needed to use the Trigo application.File location: $TOP/etc/runtime4.4 Test installation4.4.1 Start Trigo Product CenterTo start the Trigo Product Center, execute the following script:$TOP/bin/go/start_local.shThe script starts all the services required to run Trigo Product Center.Note: This process should take approximately 30-40 seconds, depending on the speed of the processor.4.4.2 Check statusRun the $TOP/bin/go/rmi_status.sh script that was provided by Trigo Product Center andverify the following services have started correctly.•admin_<machine name>•appsvr_<machine name>•eventprocessor•queuemanager•scheduler•workflowYOU HAVE SUCCESSFULLY APPLIED THE LATEST MAINTENACE RELEASE FOR TRIGO PRODUCT CENTER!NoticesIBM may not offer the products, services, or features discussed in this document in all countries. 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2015 T au r u sQuick Reference GuideThis Quick Re fe re nce Guide is not inte nde d to re place your ve hicle Owne r’s Manual which contains more de taile d information conce rning the fe ature s of your vehicle, as well as important safety warnings designed to help reduce the risk of injury to you and your passengers. Ple ase re ad your e ntire Owne r’s Manual care fully as you be gin le arning about your ne w ve hicle and re fe r to the appropriate chapte rs whe n que stions arise. All information containe d in this Quick Re fe re nce Guide was accurate at the time of duplication. We reserve the right to change features, operation and/or functionality of any vehicle specification at any time. Your Ford dealer is the be st source for the most curre nt information. For de taile d ope rating and safe ty information, ple ase consult your Owner’s Manual.November 2014 Second PrintingQuick Reference GuideTaurusLitho in U.S.A.Ford Customer Relationship Center 1-800-392-3673 (FORD)(TDD for the hearing impaired: 1-800-232-5952)@FordServiceFord Customer Relationship Centre 1-800-565-3673 (FORD)ford.ca@FordServiceCATABLE OF CONTENTSINSTRUMENT PANEL 4–5GETTING STARTEDWITH YOUR SYNC SYSTEM 6–7SYNC WITH MYFORD TOUCH 8–10COMFORT11–13CONVENIENCE 14–15FUNCTION16–17ESSENTIAL INFORMATION18–19ENTERTAINMENT NAVIGATION **BASIC COMMANDSPHONECLIMATE **W A R N I N Gford.caSOON LIGHT Lights briefly when you switch on the ignition. If it remains on or is blinking after you start INSTRUMENT2374658GETTING STARTED WITH YOUR SYNC® SYSTEMSYNC is a hands-free, voice recognition system used for entertainment, information and communication. SYNC. SAY THE WORD.BEFORE YOU GET STARTED1)S et up your owner account at (U.S.)or SyncMyRide.ca (Canada). Register by following the on-screen instructions. After registering, you can see what services you are eligible for.2)S YNC uses a wireless connection called Bluetooth®to communicate with your phone. Switch on Bluetooth mode in your phone’s menu options. This lets your phone find SYNC. If you need more details on setting up your phone to work with SYNC, visit (U.S.) or SyncMyRide.ca (Canada) or your phone manufacturer’s website.Why Do You Need a SYNC Owner Account?A SYNC owner account gives you the latest software updates that add new places, directions and information; and if you have questions, you’ll get free customer support. For additional support, refer to your Owner’s Manual, visit the website or call the toll-free number. See the inside front cover of this guide for details.PAIRING YOUR PHONE WITH SYNCIn order to use the many features of SYNC, such as making aphone call or receiving a text, you must first connect or pairyour phone with SYNC.To Pair Your Phone for the First Time1)M ake sure that your vehicle is in park (P), then switch onyour ignition and radio.2)P ress the phone button . When the display indicatesno phone is paired, press OK.3)W hen Find SYNC appears in the display, press OK.4)P ut your phone into Bluetooth discovery mode. See yourdevice’s manual, if necessary.5)W hen prompted on your phone’s display, enter the PINprovided by SYNC into your phone.6)The display indicates when the pairing is successful.The System May Prompt You to•S et your phone as primary or favorite (the primary phonereceives messages and voicemail).•D ownload your phone book (a requirement to use the fullset of voice commands).•S witch on 911 Assist®./76/GETTING STARTED WITH YOUR SYNC® SYSTEMTips•M ake sure you accept the request from SYNC to accessyour phone.•T o pair subsequent phones, please refer to Pairing Subsequent Phones in the SYNC chapter of your Owner’s Manual.•I f you are experiencing pairing problems, try performing aclean pairing by deleting your services from SYNC, deletingthe SYNC connection from your phone, and then repeatingthe Pairing Your Phone with SYNC process.USING YOUR PHONE WITH SYNCNote:Enter your phone book contacts with both first and last names to increase the ability of SYNC to select the correct contact. Remember to say the contact name exactly as it appears in your phone book.Making a Phone CallUse SYNC to make a phone call to anyone in your phone book by pressing the voice button and when prompted, give a voice command. For a list of voice commands, say “What can I say?”.For example, you could say “Call Jake Smith at home”. SYNC repeats the command back to you and dials the number. Note:You can also make phone calls by giving say voice command “Dial”, then verbally say the phone number. Answering Incoming CallsWhenever you have an incoming call, the name and number of the person calling appears in your display. Press the phone button to answer an incoming call. You can hang up at any time by pressing and holding the phone button .Do Not Disturb ModeThis feature blocks incoming calls and text messages and saves them for later. You still have access to outgoing calls when this feature is active. Say the voice command “Do not disturb on” to enable and “Do not disturb off” to disable. USING SYNC TO ACCESS DIGITAL MEDIASYNC has a media hub with multiple inputs allowing you to access personal media from your digital devices.Using Voice Commands to Play Music1)P lug your media player into your USB port.2)P ress the voice button . When prompted, say “USB”,then follow-up by saying a voice command. For a list of voice commands, say “What can I say?”.3)T he command repeats back to you and the selecteditem plays.Do MoreCreate your account at (U.S.) or SyncMyRide.ca (Canada) to get the most out of your SYNC experience. Visit the website or call the toll-free number. See the inside front cover of this guide for more details.A REVOLUTIONARY WAY TO CONNECT WITH YOUR VEHICLEon the touchscreen. For heated front seats, press repeatedly to cycle through the various heat modes and off. For cooled front seats, press repeatedly to cycle through the various cooling modes and off. If your vehicle is not equipped with a touchscreen, use The controls are on the back of the center console. Press repeatedly to cycle through the various heat settings and off. Warmer settings are indicated by more indicator lights.You can use the automatic setting toINTELLIGENT ACCESS*Note:Your intelligent access transmitter must be within 3 feet (1 meter) of the vehicle for intelligent access to function properly.To unlock a front door, pull a front exterior door handle. Once your vehicle is unlocked, you can press the exterior trunk release button near the license plate.To lock the doors, press and hold the door handle lock sensor. Allows you to lock or unlock theengine from outside your vehicle. Tostart, press and then presswithin three seconds. Your vehicleruns for 5, 10, or 15 minutes, dependingon the setting. See theFOOT PEDALS*Move the brake and acceleratorSENSING SYSTEM*This system sounds a warning AUTOMATIC TRANSMISSION* The feature gives you the abilityEASY FUEL SYSTEMpressure warning lightin your information displaywhen one or more of your With this system, push。

"model" 是一个英文单词，其用法和意义取决于上下文。

以下是一些常见的"model" 的用法和解释：
模型：在科学、工程或艺术中，一个模型可以是一个简化的表示或模拟，用于研究、设计或展示一个系统、物体或概念。

例如：建筑师可能会使用建筑模型来展示一个建筑物的设计。

时装模特：在时装和娱乐业中，"model" 通常指的是一个为设计师、摄影师或广告商展示服装、配饰或产品的人。

例如：她是一名国际知名的时装模特。

数学模型：在统计学、数学或计算机科学中，模型可以是一个数学公式、算法或计算程序，用于描述或预测系统的行为。

例如：我们使用线性回归模型来预测销售数据。

榜样：在日常用语中，"model" 也可以指一个人的行为或态度是其他人应该模仿的榜样。

例如：他一直是我们的行为模范。

型号：在产品设计中，"model" 可以指一个产品的特定版本或变种。

例如：这款手机有两个型号，一个带有更大的内存。

建模：作为一个动词，"model" 也可以表示创建或设计一个模型的过程。

例如：他们正在为新产品建模，以预测其市场反应。

这只是一些常见的"model" 的用法，实际上它在不同的领域和上下文中可能有更多的含义和用法。

MODEL S用户指南5.9文件的适用性最新软件版本发布的功能可能在本文档中未做描述，但在“发行说明”中会有描述。

触摸触摸屏上方中央“Tesla”的“T”，然后，点击“发行说明”链接，“发行说明”会显示在触摸屏上。

如果本文档中包含的信息与“发行说明”中的信息发生冲突，请以后者为准。

插图本文档中所提供的插图仅用于演示目的。

根据车辆选择、软件版本和市场区域， 您的 Model S 触摸屏上显示的信息可能会稍有不同。

产品规格在印刷时，本文档中所载的所有规格及说明已被证实是准确的。

但是，因为持续改善是特斯拉的目标，我们保留随时进行改装的权利。

错误或疏漏如需就本文档中的任何错误或疏漏进行沟通，请发送电子邮件至：ownersmanualfeedback@.©2012-2014 TESLA MOTORS, INC.保留所有权利。

本文档中的所有信息以及所有MODEL S ® 软件的版权及其他知识产权归T ESLA M OTORS 及其授权人所有。

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TESLATESLA MOTORSTESLAROADSTERMODEL S概述 (2)内部简介 (2)外观简介 (3)开启和关闭 (4)车门 (4)车窗 (8)行李箱 (9)前备箱 (11)杂物箱 (13)天窗 (14)杯托 (15)座位和安全约束系统 (16)前后排座椅 (16)座椅安全带 (18)儿童安全座椅 (21)安全气囊 (27)行驶系统 (31)驾驶员设定 (31)方向盘 (32)后视镜 (34)启动和停车 (35)挡位 (36)仪表板 (37)灯光 (43)雨刷和清洗器 (47)驻车辅助系统 (48)行程信息 (50)获得最大行驶里程 (51)制动 (52)牵引力控制 (54)巡航控制 (55)坡道起步辅助系统 (56)后视摄像头 (57)使用触摸屏 (58)触摸屏概述 (58)控制 (60)设置 (62)温度控制 (64)智能空气悬架 (67)媒体和音频系统 (68)电话 (71)安防设置 (73)连接至 Wi-Fi (74)软件更新 (75)移动应用程序 (76)充电 (77)车辆电气部件 (77)电池信息 (79)给 Model S 充电 (80)保养 (84)汽车保养时间表 (84)轮胎养护 (85)临时轮胎修理 (90)清洁 (94)雨刷片及雨刷喷水头 (97)储液罐 (98)汽车保险丝 (101)顶升和举升 (108)零配件 (109)规格 (110)识别标签 (110)车辆负载 (111)尺寸和质量 (113)子系统 (114)车轮和轮胎 (117)路边援助 (121)关于路边援助 (121)运输说明 (122)用户信息 (124)免责声明 (124)报告问题 (125)1.内门（使用内门把手 见第 6页）2.远光灯（大灯远光灯 见第 45页），转向信号灯（转向信号灯 见第 46页），雨刷及挡风玻璃清洗器（雨刷和清洗器 见第 47页）。

梨贝壳杉烯氧化酶（PpKO）三维结构的同源模建及功能预测摘要：以本试验室已克隆获得的梨贝壳杉烯氧化酶PpKO为试材，以人的微粒体细胞色素P450的A链的晶体结构为模板，综合运用生物信息学方法及分子模拟手段，构建了与其高度同源、催化功能相似的晶体结构。

通过Structure assessment和SA VS对模建结构的合理性进行了分析，结果表明利用Swiss－Model同源模建结果较好。

在此基础上，运用细胞色素P450酶系催化循环酶促动力学对PpKO的催化机理进行了初步分析，这为揭示贝壳杉烯氧化酶（KO）的生物学功能及抑制剂药物分子设计提供了有益的信息。

关键词：贝壳杉烯氧化酶；同源模建；蛋白质三维结构贝壳杉烯氧化酶（KO）是赤霉素合成途径中的关键酶（Hedden，1997），位于内质网且与叶绿体膜结合的依赖细胞色素P450(CYP450)和NADPH的单加氧酶。

通过三步连续的羟基化作用，将内根－贝壳杉烯的C－19甲基氧化，分别形成内根－贝壳杉烯醇、内根－贝壳杉烯醛和内根－贝壳杉烯酸（Helliwell，1999），该过程使6碳的B环转化为5碳的C环，从而形成赤霉素的母环结构(Lange，1998)。

NCBI保守域分析表明PpKO属于细胞色素超家族P450系。

细胞色素P450家族成员之间的一级结构差异较大，但空间结构却有着较大的相似性，含有由含亚铁血红素和半胱氨酸组成的活性中心（Rupasinghe，2006）。

目前数据库中已有经实验获得的晶体结构，较易获得模建所需的模板。

不过，我们在PDB数据库中搜索发现，目前尚无KO X光晶体衍射的晶体结构，只有拟南芥（UniProt：Q93ZB2）和赤霉菌（UniProt：A9P5P8）的同源模建晶体结构。

KO三维结构详细信息的缺失必然阻碍对其功能的理解和药物开发的滞后。

同源模拟法是根据同源蛋白质三级结构的保守性超过蛋白质序列的理论，通常在蛋白质序列上稍微的改变其三级结构亦改变很小。

SWISS-MODEL 蛋白质结构预测SWISS-MODEL是一项预测蛋白质三级结构的服务，它利用同源建模的方法实现对一段未知序列的三级结构的预测。

该服务创建于1993年,开创了自动建模的先河,并且它是讫今为止应用最广泛的免费服务之一。

同源建模法预测蛋白质三级结构一般由四步完成：1.从待测蛋白质序列出发，搜索蛋白质结构数据库（如PDB,SWISS-PROT等），得到许多相似序列（同源序列），选定其中一个（或几个）作为待测蛋白质序列的模板；2.待测蛋白质序列与选定的模板进行再次比对，插入各种可能的空位使两者的保守位置尽量对齐；3.建模：调整待测蛋白序列中主链各个原子的位置，产生与模板相同或相似的空间结构——待测蛋白质空间结构模型；4.利用能量最小化原理，使待测蛋白质侧链基团处于能量最小的位置。

最后提供给用户的是经过如上四步（或重复其中某几步）后得到的蛋白质三级结构。

SWISS-MODEL工作模式SWISS-MODEL服务器是以用户输入信息的最小化为目的设计的，即在最简单的情况下，用户仅提供一条目标蛋白的氨基酸序列。

由于比较建模程序可以具有不同的复杂性，用户输入一些额外信息对建模程序的运行有时是有必要的，比如，选择不同的模板或者调整目标模板序列比对。

该服务主要有以下三种方式:?First Approach mode(简捷模式）：这种模式提供一个简捷的用户介面：用户只需要输入一条氨基酸序列，服务器就会自动选择合适的模板。

或者，用户也可以自己指定模板（最多5条），这些模板可以来自ExPDB模板数据库（也可以是用户选择的含坐标参数的模板文件）。

如果一条模板与提交的目标序列相似度大于25%，建模程序就会自动开始运行。

但是，模板的可靠性会随着模板与目标序列之间的相似度的降低而降低，如果相似度不到50%往往就需要用手工来调整序列比对。

这种模式只能进行大于25个残基的单链蛋白三维结构预测。

?Alignment Interface（比对界面）：这种模式要求用户提供两条已经比对好的序列，并指定哪一条是目标序列，哪一条是模板序列（模板序列应该对应于ExPDB模板数据库中一条已经知道其空间结构的蛋白序列）。

第1篇一、实验目的1. 熟悉同源建模的基本原理和方法；2. 掌握同源建模的实验步骤和操作技巧；3. 通过同源建模预测蛋白质的三级结构，并验证预测结果的准确性。

二、实验原理同源建模是一种基于生物信息学的方法，利用已知蛋白质的三维结构作为模板，通过计算机模拟和计算，预测未知蛋白质的三维结构。

该方法基于以下两个原理：1. 蛋白质的结构由其氨基酸序列唯一决定，知道其一级序列，在理论上就可以获取其二级结构以及三级结构；2. 蛋白质的三级结构在进化中更稳定或者说更保守。

如果两个蛋白质的氨基酸序列有50%相同，那么约有90%的α-碳原子的位置偏差不超过3，这是同源模型化方法在结构预测方面成功的保证。

三、实验材料与仪器1. 实验材料：蛋白质序列、NCBI数据库、SwissModel在线平台、MOE软件；2. 实验仪器：计算机、网络连接。

四、实验步骤1. 收集蛋白质序列：在NCBI数据库中搜索目标蛋白质的序列，获取其一级结构信息。

2. 模板搜寻：使用SwissModel在线平台进行模板搜寻，寻找与目标蛋白质序列具有较高同源性的已知蛋白质结构作为模板。

3. 模型构建：根据模板蛋白质的三维结构，使用SwissModel在线平台构建目标蛋白质的三维结构模型。

4. 模型优化：使用MOE软件对模型进行优化，包括分子力学优化、能量最小化等。

5. 模型验证：通过比对实验结果和预测结构，验证同源建模的准确性。

6. 结果分析：分析预测结构的合理性，解释蛋白质的功能和作用机理。

五、实验结果与分析1. 模板搜寻：在SwissModel在线平台中，成功找到与目标蛋白质序列具有较高同源性的模板蛋白质。

2. 模型构建：根据模板蛋白质的三维结构，成功构建了目标蛋白质的三维结构模型。

3. 模型优化：使用MOE软件对模型进行优化，优化后的模型具有更低的能量。

4. 模型验证：通过比对实验结果和预测结构，验证同源建模的准确性。

预测结构在关键区域与实验结果基本一致。

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