Grid-enabled Virtual Screening Service User Guide - GAP
Contents
1. Translation step A Attach to the existing project 1 Generating Ligand List Quaternion step deg 2 Generating Docking Parameter File 3 Setting Job Parameters Torsion step deg 4 Job Submission Translation reduction fa Quaternion reduction fa Torsion reduction facto Close after 9 seconds Use the parameter file Users masonhsiung DC2 awk dpf3gen awk 10 3 Job Description Attach to the existing proje Resource Domain Worker Number 8 37 9 References 9 1 GAP website http gap grid sinica edu tw 9 2 EUAsiaGRID website http www euasiagrid org 9 3 EUASIaGRID voms website https vomrs grid sinica edu tw 8443 vomrs euasia vomrs 9 4 MGLTools website For preparing the target and ligands http mgltools scripps edu 382. cdi K781 1 14 02 DC2 cdi D426 1 14 0 DC2 cdi K781 7 13 97 DC2 cdi C530 1 13 75 DC2 cdi K781 1 13 73 DC2 cdi K781 1 13 73 DC2 cdi K781 1 13 57 DC2 cdi 623 0 13 54 DC2 cdi_C700 0 13 54 DC2 cdi G946 O 13 48 DC2 cdi 4159 0 Command Diane VirtualScreenin Show Best Complex Show Best Conformation Energy Threshold 0 0 Download dig Energy Histogram Get Energy List Download PDBQ Diane2 VirtualScreenin Diane2VirtualScreenin Diane2 VirtualScreenin Diane2VirtualScreenin Diane2VirtualScreenin Diane2VirtualScreenin Diane2 VirtualScreenin Diane2VirtualScreenin Submitted Time 2009 01 20 22 18 45 2009 01 20 16 51 41 2009 01 19 00 26 38 2009 01 15 22 52 56 2009 01 15 22 52 41 2009 01 15 22 52 18 2009 01 15 22 51 53 2009 01 15 22 11 27 2009 01 18 22 09 59 Success Rate 100 100 100 100 100 100 100 100 10096 Page 1 MJ gt Best Complexes _ Best Conformations Histograms gt gt Job Description Test for HC Attach to project 12 ORIAN dinaman D 14 16 14 37 DC2_TO1IAN DC2_TOLIAN 13 40 DG Show Best Co
3. 14 160 cdi K781 SeectAl SeectAl 14 020 cdi D426 14 000 cdi K781 13 970 cdi C530 13 750 cdi K781 13 730 cdi K781 13 730 cdi K781 Remove Remove 13 570 cdi K623 13 540 cdi C700 RemoveAll RemoveAll Selected 13 540 cdi G946 13 480 cdi 4159 13 380 cdi K623 13 330 cdi K781 2 13 310 cdi K623 13 300 cdi E823 0 4 13 260 cdi C708 0v Select as Control Remove Control Unselected 383 Resource Domain Con HH Worker Number 10 B Job Description 29 b Filter the ligands with a given energy threshold Initial Project Initial Project ID 22 DC2_TO1IAN A job sample for user manual Target Name Docking Parameter Ligand Selection 1 1 14 370 cdi K781 141 C Seet 14 220 cdi 8011 010 Start 1 End 383 14 160 cdi K781 155 SeletAl 14 020 cdi D426 11 14 000 cdi K781 769 Energy threshold 14 0 Remove Remove RemoveAll RemoveAll Selected Select as Control gt Select as Control gt Control Remove Control Remove Remove Control Job Description Resource Domain Worker Number 10 B Unselected c Select the ligands that you want to refine Initial Pr
4. 22 Tz _TOLIAN cdi 8011 0 14 16 DC2 cdi K781 1 14 02 DC2 cdi D426 1 14 0 DC2 cdi K781 7 13 97 DC2 cdi C530 1 cdi K781 1 gt Download PDBQ The given energy threshold is 0 0 Histogram on 1277 screens DC2 12 11 10 8 binding energy Best Complexes Best Conformations Histograms d m 11 1 8 8 3 Download the simulation results a Download the compound s PDBQ files with a given energy threshold Job View 9 Coo 9 Page 188 Job Description Job Group ID Command Submitted Time Success Rate Status A job sample for user m 1232457219103 Diane2VirtualScreeningP 2009 01 20 22 18 45 2009 01 20 16 36 20 DONE Test for HC 1232441303760 Diane2VirtualScreeningP 2009 01 20 08 59 33 DONE Attach to project 12 DC2 doman DC2_TO7IAN_doman DC2_TO6IAN_doman DC2_TOSIAN_doman DC2_TO4IAN_doman pi AN AT 2009 01 18 16 55 53 DONE 2009 01 20 16 51 41 2009 01 19 00 26 38 ONE yen DNE C PDBQ Download E Date Modified Simulation PDBQ Wednesday January 21 2009 11 00 AM 1232295613076 Diane2VirtualScreeningP File Format All Files H 8 binding energy Complexes Best Conformations Show Refine Delete C
5. cdi 3209 cdi 319 cdi 2732 4408 cdi 4476 0419 cdi 2774 0509 moe Unselected 1226 Preview Job Description Resource Domain GRID H Worker Number 10 2 8 11 4 Modify your docking parameters a There are 4 tabs for setting your docking parameter Just modify the parameters directly Predefined Project ID 22 Description A job sample for user manual Target Ligand Parameter for analysis command GA amp LGA Parameter Local Search Parameters slation step A 2 0 Quaternion step deg Torsion step deg Translation reduction factor per cycle Quaternion reduction factor per cycle Torsion reduction factor per cycle Browse Restore to default f Use the parameter file Job Description Resource Domain GRID 19 Worker Number 10 7 35 b Or you can choose to use an existing docking parameter awk file 9 DC2 awk H Date Modified Friday May 30 Predefined Project ID 22 Description A job sample for user manual 2008 9 53 PM Target Initial Factor Parameter for analysis Translation step A Quaternion step deg Torsion step deg Translation reduction factor per cycle File Format Quaternion reduction factor per cycle Torsion reduction factor per cycle Open M Use the parameter file Restore to default Job Desc
6. 04 cdi 00042895 70 cdi 000 601 Job Description Resource Domain Worker Number 18 8 4 Modify your docking parameters 8 4 1 There are 4 tabs for setting your docking parameter Just modify the parameters directly Target Ligand f Parameter for analysis command GA amp LGA Parameter Local Search Parameters Translation step Quaternion step deg 10 0 Torsion step deg 10 0 Translation reductio Quaternion reductio Torsion reduction fat Use the parameter file Browse Restore to default Job Description Resource Domain Worker Number 10 2 19 8 4 2 Or you can choose to use an existing docking parameter awk file 9 DC2_awk Date Modified pf3gen awk 10 Friday May 30 xternal grid energy Maximum allowable initial energy Maximum number of retries Open Use the parameter file Restore to default Job Description Resource Domain Worker Number 10 2 o 3 T JEAEZI Target Ligand Initial Factor Parameter for analysis command GA amp LGA Parameter Local Search Parameters e LLLI CcGAA Cluster tolerance Angstroms 1 0 External grid energy 1000 Maximum allowable initial energy 0 Maximum number of retries 10000 M Use the parameter file Users masonhsiung DC2 awk dpf3gen awk 10 Restore to default Job Description Resource Domain Worke
7. Complex Show Best Conformation Energy Threshold 0 0 12 11 10 Download dig Energy Histogram 8 binding energy Get Energy List Download PDBQ Best Complexes Best Conformations c Generate the energy list of all the best energies of the simulations C lt Page 1 Submitted Time Success Rate Status ngP 2009 01 20 22 18 45 2009 01 20 16 36 20 DONE 2009 01 20 16 51 41 2009 01 20 08 59 33 DONE 2009 01 19 00 26 38 2009 01 18 16 55 53 DONE 2009 01 15 22 52 56 2009 01 15 16 50 18 DONE M DONE DONE DONE DONE IONE Target 3 T AA pens 14 2009 4 07 PM C APDBQ Wednesday January 14 2009 11 10 AM Applications Tuesday October 28 2008 10 59 PM Swe Energy Th Id Downloaddlg Energy Histogram Get Energy List Download PDBQ 8 binding energy Best Complexes Best Conformations _ Histograms 8 9 Advanced Refinement Docking Simulation 8 9 1 Select the item you want to refine and push Refine button in the in job history window Job Description Job Group ID 15 Submitted Time Success Rate Test new refinement EUER LLL ianed in 2009 01 21 23 07 35 100 A job sample for user 1232457219103 Diane2 alScreenin 2009 01 20 22 18 45 100 1232441303760 Attach to project 12 1232295613076 DC2 doman 1232030943435 DC2 TO7lAN doman 12320
8. Total Cluster tolerance Angstroms External grid energy Maximum allowable initial energy Maximum number of retries 794 1277 60 seconds C co Start Monitoring Refresh every IV Use the parameter file n Users masonhsiung DC2 awk dpf3gen awk 10 Restore to default Job Description A job sample for user manual Resource Domain Worker Number 25 2 8 7 2 Monitor the job status via the dynamic job monitoring chart with a given refreshing interval Failed tasks Registered workers Busy workers Ready workers Failed workers Command Submitted Time Status Completed Total 2009 01 20 22 18 45 RUNNING Start Monitoring Refresh every 22 8 8 Check your docking simulation results 8 8 1 Push the job history button to popup the job history window Target Ligand all M Use the parameter file Initial Factor View 8 C lt Page jon Job Group ID Command Submitted Time Success Rate e for us 1232457219097 _doman 1232030943431 Diane2VirtualScreen doman 1232030943435 Diane2VirtualScreen 2009 01 15 22 52 100 2009 01 20 21 13 2009 01 20 16 51 2009 01 19 00 26 2009 01 15 22 52 0 100 1232030943427 1232030943423 doman AN d
9. 2 Description A job sample for user manual Ligand Docking Parameter Target Structure Default Targets FH Target Target Name Owner DC2 DEFAULT DC2_TO2IAN DEFAULT DC2_TO3IAN DEFAULT DC2_TO4IAN DEFAULT DC2 TOSIAN DEFAULT DC2 DEFAULT Nothing to visualize DC2_TO7IAN DEFAULT DC2_TO8IAN DEFAULT Job Description Resource Domain GRID HH Worker Number 10 B Submit 8 11 2 Select Target a Select the default target or your own target b Visualize the target if available and if you want Predefined Project ID 22 Description A job sample for user manual Ligand Docking Parameter Target Structure Default Targets rz Target DC2_TO1IAN Target Name Owner DC2 TOLIAN DEFAULT DC2_TO2IAN DEFAULT DC2_TO3IAN DEFAULT DC2_TO4IAN DEFAULT DC2_TOSIAN DEFAULT DEFAULT DEFAULT DEFAULT 4 Visualize TOITAN Resource Domain l GRID Worker Number 10 Submit Job Description 33 8 11 3 Select Ligands just like the ligand selection in the initial docking a Select the ligands that you want to run the docking simulation Predefined Project ID Descript Docking Parameter Library CONS cdi 3209 1023 cdi 3209 0940 Filter Rule DEMO rule P edi 4306 1056 cdi 3209 0563 lt
10. 30943431 DC2_TO6IAN_doman 1232030943427 DC2 TOSIAN doman 1232030943423 DC2 TO4IAN doman 1232023893777 DC2_TO3IAN_doman 1232023893773 8 9 2 Or press the right button of mouse to popup the popup menu and click Refinement Simulation item in the job history window Job Description Test new refinement A job sample for user Test for HC Attach to project 12 Submitted Time 2009 01 21 23 07 35 100 2009 01 20 22 18 45 100 Job Group ID Command 12325504069 Diane 2 VirtualScreenin PESEM Show simulation results 123244 2009 01 20 16 51 E 100 Success Rate 12322466 DC2 doman 12320389 M mra DC2_TO7IAN_doman DC2_TO6IAN_doman 12320309 f sals 009 01 15 22 52 18 100 1232030943423 Diane2Virtualscreenin 1232023893777 Diane2VirtualScreenin 1232023893773 Diane2VirtualScreenin DC2_TOSIAN_doman DC2_TO4IAN_doman DC2_TO3IAN_doman 8 9 3 Ligands Selection the ligands in the previous run have been sorted by each best energy Remember that the target is determined by the previous run a Filter the ligands by a range Initial Project Initial Project ID 22 A job sample for user manual Target Name DC2_TO1IAN Docking Parameter Selection 14 220 cdi 8011
11. GA Parameter Local Search Parameters Translation step A Quaternion step deg Torsion step deg Translation reduction factor per cycle Quaternion reduction factor per cycle Torsion reduction factor per cycle Use the parameter file Browse Restore to default Job Description Resource Domain GRID HH Worker Number 10 5 8 10 Configure your job 8 10 1 Input a simple job description 8 10 2 Select your resource domain 8 10 3 Decide how many workers cpus you want to use Initial Project A job sample for user manual Initial Project ID 22 Target Name DC2_TO1IAN Ligands Selection Parameter for analysis command GA amp LGA Parameter Local Search Parameters Translation step A 2 0 Quaternion step deg Torsion step deg ameter file Job Description Refinement for user manual Resource Domai Restore to default orker Number Submit 8 10 4 Push Submit button to submit the refinement simulations job Initial Project A job sample for user manual Initial Project ID 22 Target Name DC2_TO1IAN Ligands Selection Parameter for analvcic cammand CARICA Parameter lara Search Parameters Translation step A 1 Generating Ligand List Quaternion step deg 2 Generating Docking Parameter File 3 Setting Job Parameters Torsion step deg 4 Job Submissio
12. Grid Enabled Virtual Screening Service Quick User Guide 1 0 Academia Sinica Grid Computing Centre Table of Content System Hequirement Before the Installation installation After the Installation How to start GUI Client Configuration DC2 Refinement Activity GRID Service Architecture Virtual Screening Service GUI User Guide References 10 17 13 14 15 38 1 System Requirement 1 1 Windows Operating Systems Windows 2000 Windows XP Windows Vista Minimum Hardware Pentium 4 2 4 GHz Recommended Intel Core 2 Duo or greater 1 GB RAM Recommended 2 GB or greater 100 MB hard drive space JRE 1 5 required 1 2 Mac Operating Systems Mac OS X 10 3 and later Minimum Hardware Macintosh computer with an Intel x86 or PowerPC G3 G4 or G5 processor 512 MB RAM Recommended 1 GB RAM or greater 100 MB hard drive space JRE 1 5 required 1 3 Linux Operating Systems Linux with X window environment Minimum Hardware Pentium 4 2 4 GHz Recommended Intel Duo Core or greater 512 MB RAM Recommended 1 GB RAM or greater 100 MB hard drive space JRE 1 5 required 2 Before the Installation 2 1 Prepare your GRID Authority and environment 2 1 1 Certificate 2 1 1 1 Download the User Certificate Application Form a Download the User Certificate Application Form from http ca grid sinica edu tw certificate request request user cert html b Setup an interview with a local Registration Authority RA You n
13. History Job View i Show Refine Delete Page 1 WC gt C gt l Submitted Time Success Rate Status 2009 01 20 22 18 45 100 ae Job Description Job Group ID Command A job sample for user 1232457219103 Diane2VirtualScreenin Test for HC 1232441303760 Diane2VirtualScreenin 2009 01 20 16 51 41 10056 DONE Attach to project 12 1232295613076 Diane2VirtualScreenin 2009 01 19 00 26 38 100 DONE DC2 doman 1232030943435 Diane2VirtualScreenin 2009 01 15 22 52 56 10056 DONE DC2 TO7lAN doman 1232030943431 Diane2VirtualScreenin 2009 01 15 22 52 41 10056 DONE DC2_TO6IAN_doman 1232030943427 Diane2VirtualScreenin 2009 01 15 22 52 18 100 DONE DC2_TOSIAN_doman 1232030943423 Diane2VirtualScreenin 2009 01 15 22 51 53 100 DONE DC2 TO4IAN doman 1232023893777 Diane2VirtualScreenin 2009 01 15 22 11 27 10056 DONE 1232023893773 Diane VirtualScreenin DONE DC daman 2009 01 15 22 09 59 10055 A a 1 H gt Page cdi K781 1416 Energy TTE Ligand 14 22 Tz _TOLIAN cdi 8011 0 14 16 DC2 cdi K781 1 4 DC2 TOlIAN cdi D426 1 cdi K781 7 cdi C530 1 OllIAN cdi K781 1 OlIAN cdi K781 1 1 cdi K781 1 OlIAN cdi 623 0 OlIAN cdi_C700 0 1 cdi G946 0 4 cdi 4159 0 _ Show Best Conformation 0 0 Energy Thr
14. RemoveAll Li O cdi 434 1 026 Select as Control gt cdi_4341 0261 A cd 4341 0262 B Unselected Job Description Resource Domain Worker Number 10 3 b You can select the ligand as the control if you want Predefined Project ID 22 Description A job sample for user manual Target Docking Parameter Library cdi Defa b cdi 4456 3016 Sum cdi 3209 1023 cdi 4464 0973 cdi 3209 0940 Filter Rule DEMO rule b cdi 4476 1646 SelectAll cdi 3209 0563 cdi 4476 1657 cdi 3209 0557 7 567 cdi_3209 0549 cdi_3209 0531 cdi_3192 2541 lt Remove cdi_3192 2523 cdi_2827 4583 Ligand Selection lt RemoveAll Select as Control gt cdi_4341 3101 cdi 4476 0419 4476 4921 Job Description Domain Worker Number 10 B 34 c And of course you can preview the 2D structure of ligand if available by double clicking the ligand in the list Predefined Project ID 22 Description A job sample for user manual Target Library cdi Defa 5 cdi_2188 101 cdi_2191 278 Filter Rule DEMO rule cdi_2266 247 cdi_2266 248 cdi_2266 248 car mass gt 500 and mass 600 i and LogP lt 5 and donor lt 5 cdi_2266 248 and acceptor lt 10 cdi_2398 337 cdi_2539 403 cdi 2539 405 cdi 2556 2156 cdi 2556 2160 cdi 2576 4103 cdi 2677 4242 cdi 2694 4296 T Select as Control gt cdi 4341 3101 A y
15. Success Rate Status A job sample for user m 1232457219103 Diane 2 VirtualScreeningP 1 20 22 18 45 2009 01 20 16 36 20 DONE Test for HC 1232441303760 Diane2 VirtualScreeningP 01 20 16 51 41 2009 01 20 08 59 33 DONE Caneel 11 10 8 binding energy ymplexes Best Conformations Attach to project 12 1232295613076 Diane2VirtualScreeningP 2009 01 19 00 26 38 2009 01 18 16 55 53 DONE DC2_TO8IAN_doman 1232030943435 Diane2VirtualScreeningP 2009 01 15 22 52 56 2009 01 15 16 50 18 DONE DC2_TO7IAN_doman 1232030943431 Diane2VirtualScreeningP 2009 01 15 22 52 41 2009 01 15 17 04 40 DONE DC2 TO6lAN doman 1232030943427 Diane2VirtualScreeningP 2009 01 15 22 52 18 2009 01 15 16 43 37 DONE DC2 TOSIAN doman 1232030943423 Diane2VirtualScreeningP 2009 01 15 22 51 53 2009 01 15 16 45 54 DONE DC2 TO4IAN doman 1232023893777 Diane2 VirtualScreeningP 2009 01 15 22 11 27 2009 01 15 16 20 44 DONE IDC TOZIAN daman 11232N23R932773 Diane VirtialSereeninnP 2009 01 15 22 09 59 2009 01 15 16 3743 NONE J Ligand Histogram on 1277 screens DC2 TO1IAN 4 w o Downloading DC2 C708 0493 dlg file 1 96 DC2 cdi K623 0 DC2 TOlIAN cdi C700 Q DC2 TOllAN cdi G946 Q DC2 1 cdi 4159 0 N cdi K623 0 13 38 DC2 TOLIA Show Best
16. der the INSTALL PATH GVSS 1 0 0 opt gap bin execute the script e g gt INSTALL PATH GVSS 1 0 0 opt gap bin vsautodock 4 3 Mac 4 3 1 Application Bundle e Simply double click the GVSS application bundle 5 GUI Client Configuration 5 1 Show the configuration window Default Targets 4 Target Target Name VOS Client Configuration Service Advanced Metadata Service User Certificate Users masonhsiung MyPEM usercert pem User Key Users masonhsiung MyPEM userkey pem User VO euasia Job Description 5 2 Change the location of your user certificate Here you can change the location of your usercert pem and userkey pem VOS Client Configuration Service Advanced Metadata Service Users masonhsiung MyPEM usercert pem Users masonhsiung MyPEM userkey pem User VO euasia User Certificate User Key 11 5 3 Change the default VO setting the default one is euasia VOS Client Configuration Service Advanced Metadata Service User Certificate Users masonhsiung MyPEM usercert pem User Key Users masonhsiung MyPEM userkey Browse 12 6 DC2 Refinement Activity After the DC2 phase results post processing we completed the 300 000 ligands against new 8 Avian Flu variant target proteins we have estimated 20 000 ligands for DC2 refinement process Those targets are different from DC1 targets
17. e Energy Threshold 0 0 14 13 12 11 10 Download dig Energy Histogram 8 binding energy Get Energy List Download PDBQ Best Complexes Best Conformations _ Histograms b Download the dlg files the output of autodock with a given energy threshold Job Description Job Group ID Command Submitted Time Success Rate Status A job sample for user m 1232457219103 Diane2VirtualScreeningP 2009 01 20 22 18 45 2009 01 20 16 36 20 Test for HC 44 Diane2VirtualScreeninaP 2009 01 20 16 51 41 2009 08 59 Attach to project 12 DC2 doman DC2_TO7IAN_doman DC2_TO6IAN_doman DC2_TOSIAN_doman DC2 TO4IAN doman LM AN AT poste Energy Target 3 DC2 D D D D D D 14 22 DC2_TOLIA 14 16 DC2_TOLIA 14 02 DC2_TO LIA 14 0 DC2_TOLIA 13 97 DC2_TOLIA l 21 7 DC2_T0 LIAN EM ESTHER Ee Wednesday January 21 2009 2 06 PN A MW Gi simulation PDBQ Wednesday January 21 2009 2 00 PM 13 57 DC2 TOlIAI 13 54 DC2 TO1U File Format All Files Hd 13 54 DC2 TO1l 13 48 DC2_TOLIA DC2 1 Show Best Complex Show Best Conformation Energy Threshold 0 0 Download dlg Energy Histogram C Get Efergy List Download PDBQ show Reime Delete Job Description Job Group ID Command Time
18. e prepared the 20 000 ligands and 8 Avian Flu targets for the user that he she can submit job using the computing resources of EUAsiaGRID VO Moreover the user can upload himself target or ligands to do the same docking process and compare the significant result and verify in wet lab 7 GRID Service Architecture Worker Agent submission fi hut 4 e 7 Ask for a TAS and Return the Result Access application metadata Store the output ARRA METARATS CATALOGUE PROJE Access application metadata E GridFTP Storage Download the output and visualize the result Virtual Screening Service Client GUI 14 8 Virtual Screening Service GUI User Guide 8 1 Login input your VQS account and password then input the passphrase of your certificate finally decide your proxy life time Ligand Docking Parameter Target Structure User ID Password Passphrase Nothing to visualize Proxy Time a2 Hous AAAA Visualize Resource Domain Worker Number 10 B Submit Job Description ag 1 S Ligand Docking Parameter Target Structure t Targets Me User ID mason Owner DEFAULT DEFAULT Password eeeeeece Passphrase e 99999929299 Nothing to visualize Proxy Time 12 B Hours Info Login succeed Job Description Resource Domain Worke
19. ed Please feel free to contact us if you have any further questions 2009 GAP Grid Application Platform 886 2 2789 8309 rz Contact Us as Mac ASGC Academia Sinica Grid Computing 2 6 2 After you submit the application for the VQS account you will receive a notification mail and need to wait one working day for approving your application Grid enabled Virtual Screening Service GUI Client Tool 1 0 Version e Windows Standalone installer for XP and Vista e Unix Linux Standalone installer 4 e MacOS X 2009 GAP Grid Application Platform 886 2 2789 8309 A Mac ASGC Academia Sinica Grid Computing 2 6 3 Once your application is approved you will receive an email telling you that your VQS account is approved and available And follow the download link in the email to get the GUI client tool 3 Installation 3 1 Download the installer package and follow the instructions of installer Windows Double click the gvss 1 0 0 jar to startup the installer and follow the instructions from the installer to complete the installation f you are not able to startup the installer by double clicking gvss 1 0 0 jar please open the command line window and type java jar gvss 1 0 0 jar NOTE Make sure you have JRE1 5 installed on your window based system Linux Right click the gvss 1 0 0 jar and choose Open with Sun java to startup the installer Or open a terminal and type java jar gv
20. eed to meet with a ASGCCA RA to verify your identity Locate and contact your nearest RA http ca grid sinica edu tw contact html Prepare the following documents for the your interview with the RA c Complete and submit your application form 2 1 1 2 Request for certificate online Before going through 2 1 1 2 make sure that you have finished 2 1 1 1 and a CA staff has confirmed with you Create a Certificate Signing Request CSR online on CA web page http ca grid sinica edu tw certificate request nscert php Please submit request on the computer that you want to store your public private key 2 1 2 Confirm the request ASGCCA will send a confirmation to your email address Please click the url to confirm your application 2 1 3 Download and Import Your Certificate Once your certificate is issued ASGC will publish it on the website and send out a email to inform you You can simply download your certificate via the link provided in the e mail and import it into your browser 2 1 4 Export the Certificate To use your certificate you first need to export it from your browser You can find the certificate export procedure here http ca grid sinica edu tw certificate request certificate management html 2 1 5 Convert certificate to pem format for the usage of GRID To use your certificate for Grid authentication you need to convert your certificate pfx or p12 to PEM format You could find instructions here htt
21. eshold Download dig Energy Histogram Get Energy List Download PDBQ d Generate the energy histogram with controls from the best energies of all the simulations eo o Job History i Job View Hd Show Refine Delete Page 1 r gt 2 1 4 Status Success Rate 2009 01 20 16 36 20 Job Description Job Group ID Command Submitted Time A job sample for user m 1232457219103 Diane2VirtualScreeningP 2009 01 20 22 18 45 NC TO3IAN daman 2009 01 15 22 00 59 Test for HC 1232441303760 Diane2VirtualScreeningP 2009 01 20 16 51 41 2009 01 20 08 59 33 DONE Attach to project 12 1232295613076 Diane2VirtualScreeningP 2009 01 19 00 26 38 2009 01 18 16 55 53 DONE DC2 TOSIAN doman 1232030943435 Diane2VirtualScreeningP 2009 01 15 22 52 56 2009 01 15 16 50 18 DONE DC2_TO7IAN_doman 1232030943431 Diane2VirtualScreeningP 2009 01 15 22 52 41 2009 01 15 17 04 40 DONE DC2 TO6lAN doman 1232030943427 Diane2VirtualScreeningP 2009 01 15 22 52 18 2009 01 15 16 43 37 DONE DC2 TOSIAN doman 1232030943423 Diane2VirtualScreeningP 2009 01 15 22 51 53 2009 01 15 16 45 54 DONE DC2 TO4IAN doman 1232023893777 Diane2VirtualScreeningP 2009 01 15 22 11 27 2009 01 15 16 20 44 DONE 1232023RQ903773 Diane VirtualScreeninaP 2009 01 15 16 37 43 DONE Page 13 75 DC2_TO1IAN G C Energy kigand 14
22. lect gt SelectAll gt lt Remove lt RemoveAll 3A 0 96 cdi 000A 0799 cdi 000A 0800 Select as Control cdi 000A 0815 A cdi 000A 0823 x Unselected Resource Domain Worker Number 10 2 Job Description 8 3 5 Further more you can select the ligand as the control if you want o Target Docking Parameter Ligand Selection Library cdi 000A 0742 cdi 000A 0221 cdi 000A 0720 cdi 000A 0245 Filter Rule cdi 000A 0689 SelectAll gt cdi 000A 0419 di 000A 0160 cdi 000A 0430 cdi 000A 0431 cdi 000A 0506 cdi 000A 0554 Remove cdi 000A 0570 cdi 000A 0601 lt RemoveAll Select as Control gt di 000A 0102 di 000A 0800 Remove Control Job Description Resource Domain Worker Number 10 2 17 8 3 6 Double click the item of ligand you can visualize the ligand 2D structure if available Library cdi Defa 5 Filter Rule Lipinski rul Target mass gt 200 and mass lt 600 and LogP lt 5 and donor lt 5 and acceptor lt 10 cdi 000A 0742 cdi 000A 0720 cdi 000A 0689 cdi 000A 0160 cdi 000A 0155 cdi 000A 0134 cdi 000A 0111 cdi 000A 0053 cdi 000A 0024 cdi 000A 0874 cdi 000A 0796 cdi 000A 0799 cdi 000A 0815 cdi 000A 0823 cdi 000A 0829 cdi 000A 0830 Unselected Virtual Screening Service OAOA cdi 000A 0221 cdi 000A 0245 cdi 000A 0419 cdi 000A 0431 cdi 000A
23. lt rge 1 MM Job Description Job Group ID Command d Time Success Rate Status A job sample for user m 1232457219103 Diane2 VirtualScreer 01 20 22 18 45 2009 01 20 16 36 20 DONE Test for HC 1232441303760 Diane2VirtualScreen 9 01 20 16 51 41 2009 01 20 08 59 33 DONE Attach to project 12 1232295613076 Diane2 VirtualScreeni 09 01 19 00 26 38 2009 01 18 16 55 53 DONE DC2 doman 1232030943435 Diane2VirtualScreening 009 01 15 22 52 56 2009 01 15 16 50 18 DONE DC2 doman 1232030943431 Diane2VirtualScreeningP 2009 01 15 22 52 41 2009 01 15 17 04 40 DONE DC2_TO6IAN_doman 1232030943427 Diane2VirtualScreeningP 2009 01 15 22 52 18 2009 01 15 16 43 37 DONE DC2_TOSIAN_doman 1232030943423 Diane2VirtualScreeningP 2009 01 15 22 51 53 2009 01 15 16 45 54 DONE DC2 TO4IAN doman 1232023893777 Diane2VirtualScreeningP 2009 01 15 22 11 27 2009 01 15 16 20 44 DONE 93773 Diane VirtualScreeninnP 2009 01 15 22 09 59 2009 01 15 16 37 43 DONF 4 Target DC2 DC2_TO1IAN DC2_TO1IAN Downloading cdi_E715 0214 pdbq file DC2_TO1IAN DC2_TO1IAN DC2_TO1IAN DC2_TO1IAN DC2_TO1IAN DC2_TO1IAN A DC2 cdi K623 0 x DC2 cdi C700 O i DC2 cdi G946 0 DC2 TOlIAN cdi 4159 0 DC2 TOlIAN cdi K623 0 Show Best Complex Show Best Conformation e
24. mplex Show Best Conformation Energy Threshold Download dig Energy Histogram Download PDBQ N Get Energy List Job Group ID A job sample for user 1232457219103 1232441303760 1232295613076 32030943435 030943431 330943427 30943423 23893777 23893773 Job View HH Refine Delete Command Diane VirtualScreenin AN IAN cdi_K781 1 m cdi K781 1 cdi D426 1 cdi K781 7 cdi C530 1 cdi K781 1 cdi K781 1 cdi K781 1 cdi K623 0 cdi C700 0 AN cdi_G946 0 cdi_4159 0 0 0 Diane 2 VirtualScreenin 2009 01 20 22 18 45 Diane2 VirtualScreenin Diane2 VirtualScreenin Diane2 VirtualScreenin Diane2VirtualScreenin Diane2 VirtualScreenin Diane2 VirtualScreenin Diane2 VirtualScreenin Submitted Time 2009 01 20 16 51 41 2009 01 19 00 26 38 2009 01 15 22 52 56 2009 01 15 22 52 41 2009 01 15 22 52 18 2009 01 15 22 51 53 2009 01 15 22 11 27 2009 01 15 22 09 59 Page 1 H Success Rate 10096 10056 10096 100 100 100 100 100 100 gt N Status DONE DONE DONE DONE DONE DONE gt gt B A job sample for user manual DC2 TO1IAN vs cdi K781 1416 Best Complexes Best Conformations Histograms 24 c Show the best ligand conformation of a simulation Job
25. n Translation reduction f Quaternion reduction f Close after 9 seconds Torsion reduction fact C Use the parameter file I Job Description Refinement for user manual Resource Domain Worker Number 15 8 8 11 Attach more docking simulations to an existing project 8 11 1 Select the item you want to attach and press the right button of mouse to popup the popup menu and click Attach more simulations item in the job history window eoo Job Histor Job View H Show Refine Delete lt lt lt Page 1 14 Job Description Job Group ID Command Submitted Time Success Rate Status Refinement for user m 1232592256807 iDiane2VirtualScreenin 2009 01 22 12 10 11 100 DONE Test new refinement 1232550406917 Diane2VirtualScreenin 2009 01 21 23 07 35 100 DONE A job sample for user 1232457219103 Diane2 VirtualScreenin 2009 01 20 22 18 45 Test for HC 1232441303760 20 16 51 41 100 DONE Attach to project 12 123229561307 9NA19 00 26 38 100 DONE Attach more simulations T DC2 doman 123203094343 DC2 doman 1232030943431 DC2 TO6IAN doman 1232030943427 DC2 TOSIAN doman 1232030943424 rirtuarscreenim ZUC DI 15 22 52 56 100 DONE 71 15 22 52 41 100 DONE 1 15 22 52 18 100 DONE 51 53 100 DONE Predefined Project ID 2
26. oject Initial Project ID 22 A job sample for user manual Target Nag Docking Parameter Ligand Selection Se f select S SelectAll gt 12 840 cdi G397 06 12 890 cdi C073 26 Energy t 12 490 cdi K781 12 480 4386 Select as Control Remove Control 12 470 cdi G855 3 12 460 cdi E692 1 v Unselected Job Description Resource Domain Worker Number 10 B 30 d Just like the initial docking you can select one or more ligands as the controls Initial Project A job sample for user manual Initial Project ID 22 Target Name DC2_TO1IAN Docking Parameter Ligand Selection 1 1 11 070 cdi E955 1 11 210 cdi E955 10 cuim i 11 210 cdi D426 1 End 383 i 11 210 cdi E955 10 T 11 200 cdi K216 05 11 200 cdi 8013 63 11 200 cdi_C614 56 11 200 cdi_C202 07 4 11 200 cdi K403 10 v Ei 11 120 cdi_G797 0 Select as Control gt 40 cdi E955 1 Job Description 8 9 4 Modify the docking parameters for the refinement simulation just like setting parameters in the initial docking you can modify the parameters directly or just use your docking parameters awk file Initial Project A job sample for user manual Initial Project ID 22 Target Name DC2 Ligands Selection Parameter for analysis command GA amp L
27. oman Diane2VirtualScreen Diane2VirtualScreen 2009 01 15 22 52 2009 01 15 22 5 1 T 100 TO4IAN_doman ne TARIAN doman 1232023893777 1232023893773 Job Description A job sample for 8 8 2 Visualize your docking simulation results Diane2VirtualScreen Diane2VirtualScreen Diane VirtualScreen 2009 01 15 22 11 200n9 n1 185 22 n9 a Select the job you want to see and push the Show button 1232 1910 Diane 2 VirtualScreenin 2009 01 20 22 18 45 S ae 2009 01 15 22 52 56 100 DONE ener acre 2009 01 15 22 52 41 12324 3760 Diane2VirtualScreenin 2009 01 20 16 51 41 100 DONE 12322 Pe acre 2009 01 19 00 26 38 100 DONE 12320 2 18 100 DONE 100 DONE 100 DONE 100 DONE BE Biel Job Description Test for HC Attach to project 12 DC2 TOSIAN doman DC2_TO7IAN_doman DC2 TOGIAN doman DC2 TOSIAN doman DC2 TO4IAN doman ne TO3IAN doman A job sample for user Page 1 gt Job View 19 Refine Delete Job Group ID 1232457219103 1232441303760 1232295613076 1232030943435 1232030943431 1232030943427 1232030943423 1232023893777 1232023893773 Energy Target Ligand 14 37 DC2 cdi K781 1 14 22 DC2 cdi 8011 0 14 16 DC2
28. p ca grid sinica edu tw general p12toserver html For Window users you will need Win32 OpenSSL You could find this from http gnuwin32 sourceforge net packages openssl htm 2 2 GAP Environment 2 2 1 Deploy your certificate for the usage of GRID Create globus directory in your Home directory The user HOME directory on the different Operation System for example 1 Windows XP CADocument and Settings UserName 2 Mac Users UserName 3 Linux nome UserName Put your userkey pem and usercert pem on HOME globus directory On Unix like operation system HOME globus usercert pem HOME globus userkey pem HOME globus certificates On Window based operating system HOME globus usercert pem HOME globus userkey pem HOME globus certificates e NOTE A directory with prefix on Windows needs to be created by command there is no way to create such kind of directory via GUI 2 2 2 Download ASGCCA certificate PEM format Download ASGCCA http ca grid sinica edu tw publication ASGCCA pem Then rename ASGCCA pem as 9cd75687 0 and put it into globus certificates directory 2 3 You must import your certificate into your browser Then you can apply the EUAsiaGHID VO and VQS account with this browser 2 4 Join a VO After 2 1 is finished After you get your user certificate you need to join a VO for using the resource of GRID You have to apply for joining a VO with your browser which ha
29. r Number 10 2 8 5 Configure your job 8 5 1 Input a simple job description 8 5 2 Select your resource domain 8 5 3 Decide how many workers cpus you want to use fol JT TAE J Initial Factor Parameter for analysis command GA amp LGA Parameter Local Search Parameters Cluster tolerance Angstroms 1 0 External grid energy Maximum allowable i mber of a tore to default Users masonhsiung DC2 awk dpf3gen awk 16 8 6 Job submission 8 6 1 Simply push the Submit button Virtual Screening Service Target Ligand Docking Parameter A amp LGA Parameter Local Search Parameters Cluster tolerance Angi 1 Generating Ligand List External grid energy 2 Generating Docking Parameter File Maximum allowable initi 3 Setting Job Parameters 4 Job Submission SS a r Close after 6 seconds Maximum number of ret V Use the parameter file Users masonhsiung DC2_awk dpf3gen awk 10 iit Job Description A job sample for user manual Resource Domain GRID Worker Number 25 B 8 7 Job monitoring DIANE Progress Monitor master 117 103 103 51 1000 no workers 8 7 1 Push the running job monitoring buttion OCF um nn Target c Initial Factor Parameter for a lysis i A amp LGA ocal Search Params Y Command Diane2Virtus Submitted Time 2009 01 20 22 i Status RUNNING Completed
30. r Number 10 5 15 8 2 Initial Docking Simulation 8 2 1 Select Target a Select the default target or your own target b And visualize the target if available and if you want f Target Ligand Docking Parameter Target Structure Default Targets rz DC2 TO3IAN Target Target Name Owner DC2_TO1IAN DEFAULT DC2 TO2IAN DEFAULT DC2_TO3IAN DEFAULT DC2_TO4IAN DEFAULT t DEFAULT DEFAULT AULT LT 4 jc TS Job Description Resource Domain GRID H Worker Number 10 B 8 3 Select Ligands 8 3 1 Select the library 8 3 2 Select the filter rule if needed 8 3 3 And push the Filter button Library cdi 000A 0742 cdi 000A 0720 Filter Rule Lipinski rul 1 cdi 000A 0689 cdi 000A 0650 200 and mass 600 cdi 000A 0606 ogP 5 and donor lt 5 cdi 000A 0601 ceptor lt 10 cdi 000A 0570 cdi 000A 0506 cdi_000A 0431 lt RemoveAll Selected 0 cdi 000A 0430 cdi 000A 0419 cdi 000A 0245 cdi 000A 0221 Select as Control cdi 000A 0160 cdi 000A 0155 lt Remove Control Remove lt Remove Control Resource Domain GRID HH Worker Number 10 16 8 3 4 Select the ligands that you want to run the docking simulation oeg Library R Filter Rule Lipinski rul P E Docking Parameter cdi 000A 0221 cdi 000A 0245 cdi 000A 04 18 Se
31. ription Resource Domai RID Worker Number 10 2 Predefined Project ID 22 Description A job sample for user manual Best Energy 0 0 Target Ligand Initial Factor Parameter for analysis command GA amp LGA Parameter Local Search Parameters Translation step A Quaternion step deg Torsion step deg Translation reduction factor per cycle Quaternion reduction factor per cycle Torsion reduction factor per cycle IV Use the parameter file Users masonhsiung DC2_awk dpf3gen awk 10 Restore to default Job Description Resource Domain Worker Number 10 5 36 8 12 Configure your job a Input a simple job description b Select your resource domain c Decide how many workers cpus you want to use Predefined Project ID 22 Description A job sample for user manual Target Ligand Initial Factor Parameter for analysis command GA amp LGA Parameter Local Search Parameters Ss Translation step A 2 0 Quaternion step deg 10 0 Torsion step deg Translation reduction facta act M Use the parameter Users masonhsiung DC2_awk dpf3gen awk 10 Job Description Attach to the existing proje jesource Domai 8 13 Attaching docking job submission Predefined Project ID 22 Description A job sample for user manual Target Ligand Initial Facto submitting rch Parameters
32. s your certificate euasia https vomrs grid sinica edu tw 8443 vomrs euasia vomrs 2 5 Make sure you have Java Runtime Environment JRE1 5 installed 2 6 Apply for a VQS account for using this Virtual Screening Service 2 6 1 Apply via https vl01 grid sinica edu tw 8443 vqsreg Please make sure the browser you used contains your user certificate the server will detect the user certificate and retrieve the DN Distinguishing Name from the user certificate for the registration a ra Fa S https t 04 grid sinica edu tw 8443 vqsreg webpages vqsRegForm jsp Qr Google VQS Account Registration Title Full Name Y our Account Y our Password Contirm Password E mail Country S Address Phone Affiliation Your current certificate is CZTW O ZAS OUZGRID CN Mason Hsiung 148117 certified by C TW O AS CN Academia Sinica Grid Computing Certification Authority Mercury 2009 GAP Grid Application Platform 886 2 2789 8309 Contact Us ASGC Academia Sinica Grid Computing NOTE Please select the corresponding VO Virtual Organization you belong to wn Fa S https t 04 grid sinica edu tw 8443 vqsreg webpages vqsRegContro Qr Google We have received your application Thank you for your registration Your information is going to be verified Please wait one working day We will send you an e mail after your application is approv
33. ss 1 0 0 jar NOTE Make sure you have JRE1 5 installed on your Linux Mac Double click gvss 1 0 0 dmg and drag the GVSS application to Applications folder or any place you want 3 2 GAP environment 3 2 1 GAP HOME environment variable You don t really have to modify this variable manually the installer will set the GAP HOME variable automatically 3 2 2 Since this service is based on GAP and GAP uses globus toolkit by default the GUI client will try to find your user certificate usercert pem and userkey pem under HOME globus Please make sure you have followed the previous instruction to put your user certificate into the right directory Or you could change the location of the usercert pem and userkey pem later through the GUI 4 After the Installation How to start 4 1 Windows 4 1 1 Desktop Shortcut After the installation there will be a shortcut icon created for quick launching this GUI client 4 1 2 The startup batch script vsautodock bat The will be a startup batch script under the INSTALL_PATH GVSS 1 0 0 opt gap bin execute the script eg C INSTALL_PATH GVSS 1 0 0 opt gap bin vsautodock Or double click the batch script to launch this GUI client 4 2 Linux 4 2 1 Desktop Shortcut After the installation there will be a shortcut icon created for quick launching this GUI client 4 2 2 The startup bash script vsautodock The will be a startup bash script un
34. that we successfully demonstrated in 2006 The targets are based on X ray determined structure and 2 types of conformation The 8 mutations of target divided into 2 categories 1 Closed Form a DC2_TO1IAN b DC2 TO2IAN c DC2 TOS3IAN d DC2 TOAIAN 2 Open Form a DC2_TO5IAN b DC2 DC2 d DC2 For the DC2 refinement activity we have extracted the best 20 000 compounds from the results of DC2 initial docking activity The 20 000 compounds extracting from the previous DC2 initial docking And these compounds will be divided into 1 000 data sets DOR 0001 1000 for different EUAsiaGRID partners 1 Here we provide a web page for subscribing your data sets which you want to process and the feedback of the current running progress https vl01 grid sinica edu tw 8443 dc2refine 2 You can process these data sets one by one each data set contains 20 ligands 20 tasks However we basically recommend you processing 10 or more data sets 200 tasks at a time This will make you use the computing resource more efficiently We developed the Stand alone GUI for using virtual screening service based on GAP Grid Application Platform The software packages integrated the EGEE gLite software DIANE2 and AMGA and used the Autodock as the simulation docking engine User can submit computing jobs when the user selects the target and ligands in grid environment Therefore the DC2 refinement that w
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