Grid-Enabled Virtual Screening Service Quick User Guide 1 .0.1
Contents
1. We have received your application Thank you for your registration Your informaton is going to be versfied Please wait one working day We will sead you an e mail afier yowr apphcanon is appeoved Picase foel free to contact us if you have any further questions 209 GAP Gnd Appicanon Platfoem o58 2 2 789 49 E Contact Us x ASGC Academi 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 ee ES 1 ot co Bia Bhai tetps gap grid sina edu tm 8443 vgnreg htmi vasRegForm temi Ea come 9 Downloads Grid enabled Virtual Screening Service GUI Client Tool 1 0 Version done installer for XP and Vit Vow Linus vundabac inctalk 2009 GAP Grid Application Plafon 556 2 2 789 549 a ASGC Academia Sinica Grid Computing 3 Installation 3 1 Download the installer package and follow the instructions of installer e Windows e Double click the gvss 1 0 0 jar to startup the installer and follow the instructions from the installer to complete the installation If 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 e NOTE Make sure you have JRE1 5 installed on your window based system e Linux e Right click the gvss 1 0 02. Target Struct mason Nothing 10 vitwabre C0 WB woer numer AG uo 7 2 Initial Docking Simulation 7 2 1 Select Target a Select the default target or your own target b And visualize the target if available and if you want Wa Target Legand Decking Parameter Target Soructere Defasit Targets a Target OC TOMAN Target have Urea cx TOLMAN DEFALI DCJ TOJAN DEFAUL OCZ TOSIAAN DEFAULT 7 DEFAULT PAAT at aT ey pos Reroute Doman CHO H Worker Number 7 3 Select Ligands 7 3 1 Select the library 7 3 2 Select the filter rule if needed 7 3 3 And push the Filter button BG ong m 1 9 Target Ugeni Decking Pare lt s 200 aed mass lt 600 gf lt 5 and donat lt 5 ceptor lt DIN odi DOOA O7 42 odi 004 0720 ordi 0901 0649 od OSOA 0650 ordi 0004 0606 id DOD 0801 cdi 0001 0570 cd 0004 0554 lt Remove p i 0001 0906 3 ana me e Remevens Selected D pdi ODQA 04 10 od 0901 0419 odi OOOA O2 45 od DOOA O2271 Setect as Contre gt odi 0904 0160 edi 0004 0155 lt Remove Cornros deselected j Prevesa Rerource Doman CHO H Worker Number 10 57 Submit 15 7 3 4 Select the ligands that you want to run the docking simulation cdi O90A 0221 Odi 0804 0243 cdi OJOA 0 odi 09g odi 04i 0904 0799 D odi 0904 0615 ci
3. 32 7 10 3 Select Ligands just like the ligand selection in the initial docking a Select the ligands that you want to run the docking simulation Docking Parameter oo cdi 3209 1023 odi 3209 0940 cdi 1209 8961 cdi 4306 1056 adi 4341 0260 cdi 4341 0261 cdi 4141 9742 b You can select the ligand as the control if you want qai 4454 1016 adi 3209 1023 cdi 4464 0975 cdi 4476 1646 cdi 4476 1657 cdi 4476 4919 odi 3209 0940 cd 1709 0561 tdi 5209 05357 odi 3209 0549 cdi 1209 8811 cdi 3192 2941 odi 3192 2823 cdi 7827 4961 adi 4Ja1 3LOt cdi 4476 0419 cdi 4476 4921 c And of course you can preview the 2D structure of ligand if available by double clicking the ligand in the list ekeke Predefined Project ID 22 Description A jo sample for user manual Le er r T r Library Cdi Deta cdi 2144 101 cdi 2191 278 filter Rule DIMOrule 8 cdi 2266 247 cd 2266 248 Imass gt 500 and mass lt 600 con 2266 245 an and iLog lt and idomor lt cdi 2266 248 cdi 3209 j and acceptor lt 10 cdi 2394 357 cdi 319 cdi 2539 405 cah 2519 405 cdi 7996 2196 cadi 2996 4160 cdi 7576 4103 C1 2694 4296 nasa co cdi 4476 0419 cdi 2732 4408 Unselected 1226 jed Description Resowce Domain CRID 41 Worker Number ng Suam 7 10 4 Modify your docking
4. You need 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 Reguest 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 Reguest CSR online on CA web page http ca grid sinica edu tw certificate reguest nscert php Please submit reguest on the computer that you want to store your public private key 2 1 2 Confirm the reguest 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 reguest 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
5. v te S id Aj en a 5 Was MA ab ere fer ane menon Pee 1 l4 Iei E s r Pre ww re map ors mT il Pen 7 8 3 Download the simulation results a Download the compound s PDBQ files with a given energy threshold pb View 6 Canon eter Cor ma UG gt Ta aan Test for HE ARAA proper i OCZ TOJAN doman ix TOTAR domas OCI TOUMA domas ix TOSAN domas CIL TOCNA Gores NG TOMA Arman 1252441501700 Rene TELI on Tan oran wee amp Test tr mat 1232441501700 Aman we progect it II Mei ion DC2 TOSAN doman 1252030943455 tx TOTAR domas il 42010704 laki OCI TOSAR doman 1252030943477 DC TOSAN domaa II 1701074 MI CIL TOCA Gores 11 5002 9099377 LIL Leet TPA pa Sa Onee Ai OCJ TONAN OC2_ TOLMAN OCI TOAN OCZ TONAN DCJ TONAN OCJ TONAN DCJ TOAN OCJ TOL DCJ TOLAN OCJ TOAN OCZ TOLMAN OCI _TOLAN OCZ TOAN eweseenE CEREERE ood Te Deane Vrtustkreenng 2009 01 20 16 91 41 Sent PemaakareeraaP 1099 91 19 CO 16 J8 1009 81 18 16 IA 48 lowe 1 20 1631 41 31 19 00 26 ts 1 13 22352 20 01 14 JF Spat 2099 41 13 2752 18 2008 01 15 27 4148 100081519 22 11 47 1fwrS 41 14 PP ira ta roe CA gt Ct barem h 2009 01 20 08 19 55 Com cane re MC gt ea bance Gam 2009 01 20 06 39 55 1009 01 18 169645 1099 41 11 1630 18 2008 01 14 17 Ge 40 2099 91 13 16 5 7 2009 01 15
6. 16 44 44 1099 91 15 16 79 s vwee 01 1 18 UP 48 cEERERES b Download the dlg files the output of autodock with a given energy threshold pomm iB son Cat 000 feb Tete pees Test tor WC Amih Op proget 14 DCJ TOSAN doman OK TOTUN dear DCJ TOGN doman DCILTOSMN Gerer DCJ TOSAN doman ne INLAN Ame bob Deets tapa Test tor HC 1232441503760 Chew letanp 1 29 265141 2009 01 200659 55 DONE Anti Do proget 14 TETTEL TEOT Chere A E E ai DE bP COLE 1S JOOS 01 16 165543 Dore DCI TOSAN domar 1232030941455 Chae raomp 01 15 225236 2009 01 15 1630 18 DONE 1X1 _ TOAN denagn 123703094343 Deva 0O05 2252 4 POOR Oh 1S 17 Os MG DORE DCI TOCAN daran 1212010941427 Domita 2008 01 15 22 52 18 2009 01 15 164557 DONE D2 _TOUMAN German 1237030943423 Cee V OOS 225155 200 0115 1646534 DOnt DCJ TOSAN domas 1212021841777 Donelsen 2008 01 15 22 1127 2009 01 15 162044 DONE mm INEAN Awe tJ tm tny Tee Tentang eee PERG 88 23 eav NUN ME MU 1K UP 24 wwe oa me GW gt DC 21 wamre Bate show Aetna 00m ph Ca mag oi Page Year sees Bate Umur ae Co Co w 471 0 15 54 OCZ TONAN amp C790 0 15 ya ee oA LYA6 9 1145 OCZ TOIAN lt a alspa S 13 4 OC TOLMAN oa iiron S oses SE CSREES c Generate the energy list of all the best energies of the simulations ome DMC t
7. C From Target Tarball Target Tarball 39 b From a well packaged target tarball 1 Select the target tarball Target Name New TaroetName Target Data Source From arbitrary directory Target PDBQS iasonhsiumg Desktop CVSS_release Dengue Dengue_ NS3 Dengue NS3 pdbgs Browse Target Maps Users masonhsiung Desktop CVSS release Dengue Dengue NS3 where contains maps Nd maps xyz and X ap Target Name browse From Target Tarball Target Tarball 2 System will check the content of the tarball If the tarball is invalid you will not be allowed to select the tarball The target name will be changed according to this tarballs target name Dengue NS3L POBOS file Dengue NS3 pdbgs Total map files Dengue NS LA map Dengue_NS3 5 map The fid file Dengue _NS3 maps fid The xyz file Dengue NSI maps xyz 3 The target name will be determined automatically according to the target tarball You are not able to change it Target Data Source C From arbitrary directory Target PDBQS iasonhsiumg Desktop CVSS_release Dengue Dengue_ NS3 Dengue NS3 pdbgs Growse Target Maps Users masonhsiung Desktop CVSS release Dengue Dengue NS3 where contains maps fid maps xyz and X map Target Name Browse From Target Tarball Target Tarball Users masonhsiung Desktop CVSS_release Dengue Dengue_NS3 tar gz 4 Finally simply press the register button to upload and regis
8. browser which has your certificate e 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 vI01 grid sinica edu tw 8443 vgsreg 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 ab ma mps t O4 gnd sinica edu tw 443 vgsreg webpages vgskegForm jso KQ Googe Oyama VQS Account Registration Full Name Your Account Your Password Condirm Passwoed E mail Country Address Phone Aftilianon VO esama Subt Reset Your current certificate is Ce TWIO AS OUrFGRID ON Mason Hsiung 148117 certified by Ca TWOSASI CNe Academia Sinica Grid Computing Certification Authority Mercury 2009 GAP Grid Application Platform 4 586 2 2 789 45 309 Contact Us N asx ASGC Academia Sinica Grid Computing e NOTE Please select the corresponding VO Virtual Organization you belong to 2 6 2 After you submit the application for the VAS account you will receive a notification mail and need to wait one working day for approving your application saj NS he eS terms 1 1 04 grid sina eds tw B44 3 wqureg mebpages eqsRegcontro MQ boon 9
9. jar and choose Open with Sun java to startup the installer Or open a terminal and type java jar gvss 1 0 0 jar e NOTE Make sure you have JRE1 5 installed on your Linux e Mac e 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 e 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 e 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 e The will be a startup batch script under the INSTALL_PATH GVSS 1 0 0 opt gap bin execute the script eg C5 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 qui
10. run a Filter the ligands by a range 14 570 0i K761 14 220 csi 801 teisen krsi selectai gt 14 070 oft D4276 14 000 of K781 119701 cdi C3 pO 15 750 0f K781 II TIO 0 K781 43 7301 ce K781 L3 370 0f Ke2 1340 cec700 C lt Removean Selected o L3 340 ofi C946 IL AKI o 4148 TEMU IN KOT Opa jer ea hE S10 0f tan 13 500 ct 0523 0 4 1 1260 o C7OE O y s Umuterted Kerource Domain 28 b Filter the ligands with a given energy threshold initial Project A jab sample for user manual ional Proect D 22 Target Name DC TOLMAN Decking Parameter lt 4 370 cdi K781 141 14 2201 csi 8011 010 Start 1 Ing 14 Pe 160 om KPS 1199 24 020 ch D476 1 14 140001 ci KPS 1 769 c Select the ligands that you want to refine Initial Project A jab sample for user manual inal Propet iD 22 ee Liparre etet fic Per o 12 840 c amp t_C 597 04 h2 S90 ca 0071 2 22 890 om 7155 17 9101 si 23 Int se PLOT I LL AYO of 781 12 480 os 41 h2 480 og K784 si 470 edi CSI 4 2 440 8682 1 s 8 r Unielected 347 om Revource Domain C IG Worker Number 10 C1 Semen 29 d Just like the initial docking you can select one or more ligands as the controls Dec
11. 000A 0823 a C lt temove Cones odi_0004 0742 Odi 0904 0720 cdi 0904 06459 di 0904 0160 cdi 0904 0221 cdi 0904 0245 cdi 0901 0419 cdi 0904 0430 cdi 0004 0411 cdi 0004 0506 cdi 0004 0554 7 3 6 Double click the item of ligand you can visualize the ligand 2D structure if available Laka Virtual S lt service Library Cedi iDeta 3 cai 00 0742 cdi 0004 0719 Fiker Rule Upaski rul adi 0001 0659 adi 000 016 Imans gt 200 and mass lt 6001 cdi 0001 0155 and Log lt 5 and doner lt cdi 0001 0134 land lacceptor lt 10 cdi 0004 0111 cdi 0004 0053 adi 0004 0024 cdi 0004 0874 cdi 0001 0794 cdi 0004 0799 cdi 0004 0615 cdi 0004 0625 cdi 0001 0879 cdi 0004 0610 17 7 4 Modify your docking parameters 7 4 1 There are 4 tabs for setting your docking parameter Just modify the parameters directly 7 4 2 Or you can choose to use an existing docking parameter awk file OC2_awk H O00 Ging for anabysis Mar cemum atowable sana energy Maxemum number of retries wengi iretial Factor Parameter fer analysis command CASLCA Parameter Local Search Parameters Cluster tolerance Aegstroms External grod energy Maximum allowable iretial energy Maximum sumber of retries 7 5 Configure your job 7 5 1 Input a simple job description 7 5 2 Select your resource domain 7 5 3 Decide how many workers cpus you want to use UG _fnmtia
12. Grid Enabled Virtual Screening Service Quick User Guide 1 0 1 Academia Sinica Grid Computing Centre Table of Content System Requirement Before the Installation Installation After the Installation How to start GUI Client Configuration GRID Service Architecture Virtual Screening Service GUI User Guide Upload your own target and ligands References 10 17 13 37 44 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 reguest reguest user cert htmi b Setup an interview with a local Registration Authority RA
13. ck launching this GUI client 4 2 2 The startup bash script vsautodock e The will be a startup bash script under the INSTALL_PATH GVSS 1 0 0 opt gap bin execute the script e g 5 SINSTALL 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 toga Serexe Advarxed Metadata Service Kate tone ners ma tanding MyPEM ureri ty gem omwwse 5 2 Change the location of your user certificate e Here you can change the location of your usercert pem and userkey pem Trens marsen MyPEM ertey gem Sowse 5 3 Change the default VO setting the default one is euasia Service Advanced 9 Metadata Service User Cerificate Users mas onteaseng MyPEM wrercert pemi trome User Key Users masenhsiung MpPEM userkey 6 browse 6 GRID Service Architecture Return the Result Access application metadata Store the output A p X ARDA METADATA CATALOGLE PROJECT b Access application metadata Download the output and visualize the result 7 Virtual Screening Service GUI User Guide 7 1 Login input your VQS account and password then input the passphrase of your certificate finally decide your proxy life time Target Struct Nothing 10 vitwabre f visualize GRID MG Worker Number 10 el Submit
14. here http ca grid sinica edu tw general p12toserver html For Window users you will need e Win32 OpenSSL e 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 YsHOMESA globusicertificates 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 9cd75e87 0 and put it into globus certificates directory 2 3 You must import your certificate into your browser Then you can apply the EUAsiaGRID 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
15. king Parameter 21 070 ci _6955 1 11210 ca 6955 10 1 1 070 cet 6955 1 11 210 c 0426 1 1LOS0 cdi 501 4 1 210 oh E99S 10 1 090 cdi K254 1 200 ca K7 6 05 11 090 of Cats bh 1200 oi S01 3 6 G0 csi C7 13 0 1200 o _C202 07 11 200 c K403 10 11 120 w On 40 cdi E955 7 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 Penject A job sample for uter manual initial Project ID 22 Target Name DC2 TONAN gan seneton Oocking Parameter Translation stap A Quatermon step deg Torsion map dag Translation seduction factor J per cycle Quatermon reduction factor per cycle Torsion seduction factor J per cycle 7 9 5 Configure your job a Input a simple job description b Select your resource domain c Decide how many workers cpus you want to use Initial Praject A job sample far user manual Initial Project ID 72 Target Name DC2 TONAN 7 9 6 Push Submit button to submit the refinement simulations job Initial Peaject A jab sample for uter manual Initial Project ID 22 Target Name DC2_TOLAN 7 10 Attach more docking simulations to an existing project 7 10 1 Select the item you want to attach and press the right button of mouse to popup the popup menu and click Attach mo
16. l Factor Parameter for analysis command GAMGA Parameter Local Search Paramesers Cluster tolerance Angitroema sternal god erergy Macimun sT owahe 7 6 Job submission 7 6 1 Simply push the Submit button OOO Civiter tolerance Angs External grid energy Masemum allowable Maxemum number of Z Use the parameter file Users masenhsiung OC2_awk dpi3genawk 10 browse Restore to deli job Description A job rampie fer user mansai Resource Domain GRID Worker Number 3516 7 7 J0b monitoring 7 7 1 Push the running job monitoring buttion pr OE Initial Factor Parameter for Rat eek Cluster tolerance Angutroen Uaternal god erergy Maximum allowable intial energy Maximum sumber of retries 7 7 2 Monitor the job status via the dynamic job monitoring chart with a given refreshing interval DIANE Progress Monitor master 117 103 103 51 10003 7 8 Check your docking simulation results 7 8 1 Push the job history button to popup the job history window eb Come O 14170972 10007 1202441903700 2 UNDIN iJ 70 boee 1415 is ho nga nahi IA NG 9994 2437 125209994342 1252025893777 teh TT LIEAA kta few 1999 94 49 41 89 2009 01 20 1651 5000 01 19 00 24 SO00 GL it 3143 pOoe 0b 16 22 82 2000 01 15 27 11 5 1998 06 19 44 92 2099 94 13 242 51 MASAI 1 2 48 job Description A job sampe for 7 8 2 Visualize your docking simu
17. lation results a Select the job you want to see and push the Show button 1g P FEFEFE mno wa 2009 01 20 1631 et 100 12122 _ 2009 01 19 00 26 BS 100 io 2009 91 11 22 11 14 100 t2320 2009 01 15 224241 100 i293 z is 100 42320 3 100 kena 1 100 hb tm ta lata ear tens Bete Dune Virus Ea ree rer C Ate amp Greet iJ 410108 A0 ra Dure Yuta PK teen OOF OL1 19 OO 26 8 1001 DCJ TOCAN domon 12120 00943415 Dune Vwmuetcreemm J009 01 15 22 52734 100 DCJ TOTMAN Gover 173209096345 Durel Vraa Dieten 0908 01 19 22 52 Al 10m J LOAN Dewa Pe Pith i Pay Lute Vw Pa lee ee JO09 0 527237 148 10m DCI OMAN Gover 173209096347353 Deere Vranas 2009 01 15 225135 10m In DOAN Opmar EPFPLTSIS EPET Duse Vw PW i te an gt 3 4 i m Thilak Awnrer POPAT i Pee Dua re J tere he ree rer Lu MAA AL IAPA i A T T ager L pano 14 57 DCJ TOLMAN aa E7S1 1 Adi Ind TOLMAN ee BAIT 1 0 14 146 DCJ TOLMAN A KTE la Ol ix TOLMAN im baju lag DCJ TOLMAN cA Te 1597 DCJ TOLMAN A Coil bars DCJ TOLMAN ce_arei i 15 73 DCJ TOLMAN A amp 78i 1 Ia ys J TOAN A Kalo 15937 DCJ TOLAN lt coe_8621 0 IS ya ix TOLAN om CTOO O 18 44 DCJ TOLAN a CWw O Sir 15 45 OCJ TODAN di 159 0 Shore Rect Corgpex Shore Best C ovtorrration Erergy Threvhet Dore toed dtg terergy Hniogrerm Cat Enesgy List Dowetosd PORC GestCempieres beni Cor
18. ngue_NS3 Dengue NS3 pdbgs Target Maps twhere contains maps C From Target Tarball Target Tarball 2 Select the directory which contains the target s map xyz and fld files NOTE Make sure the map xyz and fld files are under the directory otherwise you will not be allowed to select the directory rage Mam Target Data Source From arbitrary directory Target PDOBQS iasonhsiumg Desktop CVSS_release Dengue Dengue_ NS3 Dengue_NS3 pdbas Target Maps Users masonihnsiung Desktop CVSS release Dengue Dengue NSJ3 iwhere contains maps fid maps C From Target Tarball Target Tarball 3 Name this target this will automatically replace the old target name with the new name in all the files pdbgs map xyz Target Data Source From arbitrary directory Target PDBQS iasonhsiumg Desktop CVSS_release Dengue Dengue_ NS3 Dengue NS3 pdbgs Target Maps Users masonhsiung Desktop CVSS release Dengue Dengue NS3 where contains maps id maps xyz and X map Target Name C From Target Tarball Target Tarball 4 Finally simply press the register button to upload and register your own target Target Name Target Data Source From arbitrary directory Target PDBQS iasonhsiung Desktop CVSS_release Dengue Dengue_ NS3 Dengue NS3 pdbgs Target Maps Users masonhsiung Desktop CVSS release Dengue Dengue NS3 where contains maps id maps xyz and X map Target Name
19. parameters a There are 4 tabs for setting your docking parameter Just modify the parameters directly Predefined Project WM 22 Description A job sample for uter manusi ia Parameter for analysis command GAMLGA Parameter Local Search Parameters Lo Torsion stepi deg Translation reduction factor per cycle Qusternion redection factor per cycle Torsion reduction tactor per cycle 34 b Or you can choose to use an existing docking parameter awk file Predefined Project ID 22 Description A job sample for user manual Target intial Factor Parameter for Tramsiation step JA Quatermon srep deg Torsion step deg Translation reduction factor per cycle Quatermon reduction factor per cycle Torsion reduction factor per cycle i Use the parameter file job Description Predefined Project 10 22 Description A job sample for user manual Traralatios step JA Ouaterreon step deg Torsion step deg Trasalanioa reduction factor per cycle Quaterreon reduction factor per cycle Torsion reduction factor per cycle Use the parameter file Users masenhsieng DC2_awk dpl3gen awk 10 jb Desctgtion SS Domain GR eter Member 1016 CS 35 7 10 5 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 10 22 Descri
20. ption A job sample for uter manual e gn ng Ram pa inma Fanos Parameter for analysis command GASLGA Parameter Local Search Parameter Translation step A 70 Qustermen step deg Torsion step deg Translation reduction facte Users marenhaung OC2 awk dpligenawk t0 job Description Attach to the existing prope Besource C MM Use the parameter Predefined Project 10 22 Description A job sample for uter manual Translation step A Qumtermon step deg Torsion step deg Translation reduction f Quaternion reduction Torsion reduction tacto MM Use the parameter file Users marenhuung DC2 awk dpf igen awk 10 Jab Description Attach to the existing prow Resource Domain Worker Number Caj C saom j 36 8 Upload your own target and ligands 8 1 Upload your own target 8 1 1 Press the target upload button Opan Detavit Targul Target Docking Parameter Target Hare Oc TONAN DC2 TOZUN DCJ TOIAN DC TOIAN DCZ TOSIAAN OC2_TOGIAN DCJ TO7UN DC TONAN Dengue N53 Chome DC2_TONIAN OC TOIAN where contains maps fid maps xyz and map Target Name bowie OC TOSIAAN a From arbitrary directory Please do this on Linux unless you are sure your target map files are fine on case insensitive OS 1 Select the target s pdbgs Target Name Target Data Source From arbitrary directory Target PDBQS iasonhsiunmg Desktop CVSS_release Dengue De
21. re simulations item in the job history window Ana job View i Seow Anima Orete Page 1 H gt gt gt gt joo Dis ec gen b Group O omar bamad T ane Seccese Aate atar Retrersent for weer m 1712592756807 Disnea Veteatacreemm 1009 01 42 12 101 10031 DONI Tat new cefrermeret 1212550406617 Diana 2Vutuarreean 2003 01 71 710715 100 DONI Tew tor Pe 6414 1003 DONT Atach to project 12 l 190026 38 1001 DONI OC TOMAN domar 12320 32 18 100 DONI Dt TOJAN domar 12 200 pe 225241 Lara DONI DC TONAN domar 1212 Delete job 01 15 2252 18 Loos DONE l i MOL 15 22 5133 Looe DONE M2 TOSIAAN domar 2 3 Dese Vetus Arn Pedag Pena O N Deetreoties A po names for weer ere iwon E Dach ong Par aortas P r Refedt 7 aH yet tractans sngat e ga ams _ se 1 AN Wia Tc AA tia 1E IAA 4 san pera ar feta TEORA oeras va Png we rttwewe AN 4 L an ate Vrest oe bi Ovi cagpoae berora Doner CO EZ Wote wat om 7 10 2 Select Target a Select the default target or your own target b Visualize the target if available and if you want Predefined Project 10 22 A job sample for wer manual Target Ligaed Docking Parameter Target Structure Descriptio s Default Targets Target DOZ TONAN Target herve Crerar DC OC2_ 103 DC 1O41 DC DC2 TOMAN Resource Donain LRO a Worker Number 10 8 Seber lab Description
22. ring the target and ligands http mgltools scripps edu 44
23. ter your own target Target Name Target Data Source From arbitrary directory Target POBQS iasonhsiung Desktop CVSS_release Dengue Dengue_ NS3 Dengue_NS3 pdbas krowse Target Maps Users masonhsiung Desktop CVSS release Dengue Dengue NS3 twhere contains maps fid maps xyz and X ap Target Name browse From Target Tarball Target Tarball Users masc Dengue NSJ tar gz 41 8 2 Upload your own ligands 8 2 1 Press the ligand upload button Resowce Domain GRO HB Worker Number 10 8 2 2 Decide either you want to create a compound library or attach to an existing Compound library 42 8 2 3 Select the directory which contains your compound PDBQ data New Library MyCompound If you Attach to an existing Library PDBQ Directory Users masonhsiung BPDBO where contains your compound PDBO datz 8 2 4 Finally simply press the register button to upload and register all the Compounds under the directory New Library MyCompound If you want to share this library C Shared Attach to an existing Library f O PDBQ Directory Users masonhsiung BPDBO where contains your compound PDBO data 43 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 prepa
24. tormetors Histogram b Show the best complex of a simulation bod view l Shere l net Deter Page 1 i wees Oe Dene 2 vra Ek ree rer Taat Tan wa Ik 34041 UI rat Me Pela Pe rear ior ieJ0O 165141 1001 DOA Azat o prer 14 Parra b GOLION thaws vna lki ten 7909 01 19 00 26 14 100 DONI 252090043455 Thane WetueExreere 2009 91 15 22 31 168 100 DOAI NGEL 1414421 Leet Vu tang Ml ee rou leit 725241 1007 IMA 1104 1423 Themes wwe Fe ree ar 1000 91 19 2 52 14 100 DOM 0941421 Dese PW rta Exreere 1009 91 19 24291193 100 DOAI bawaan Ore Vu tan TM ee A fur Dire iJ jon LI A Sawan Then Se wth ae er reen wre lais 22 Ia 59 10n eA 3 AN Show Sau Compex Show 814 L orvtorreetion trergy Theres Peni Download dig Lrergy Htittograrn Cat trerey Lim Dwnload PDS Rest Coalormunont 45 6 1 Oqpt are 23 c Show the best ligand conformation of a simulation Ano Jeb uory haves W shew Refine Derete nga Ci W j rE amp amp S s gt EET s 1 4 D A terry f tres hadd Download chy Imer reog Cat bner USt Dew lega PON d Generate the energy histogram with controls from the best energies of all the simulations AND yaa re prs 84 ra Cat ag iriste Page wea if 44 4 I 4 Put Ar i F n 4 4 3 AJ AN 4 ame A i i 3 Aj A i 4 pmi g 2 s Ai A j v4 j i 4 4 Pad Ly 4 i 4 i a Ai tA i
25. wncees ana Matet pete eb me 2000 01 26 16514 1009 01 20 OM II DONI 2907 01 19 002655 2009 01 15 163553 DONE DOOP OL 35 225256 2000 01 15 16 0 Li DONI Wedresday jarsanry 14 2009 4 07 FM Wednesday Jarsanry 14 2009 11 10 AM Tusuday October 74 POOR 10 59 PM 7 9 Advanced Refinement Docking Simulation 7 9 1 Select the item you want to refine and push Refine button in the in job history window bot Oeste preon bet Croep O Sesbretiod Tere Seccess fate Test sem referent 1232550406917 Oua creeren 2009 01 71 2307 35 100 Test tor HC 1232441303760 Anah te project 12 123229561 2076 DCZ TOSUN doman 1232050945415 DC2 TOTMN doman 1232030943431 12120094 5427 1232030943423 1212071491777 DC TOSUN doman 1232023493773 7 9 2 Or press the right button of mouse to popup the popup menu and click Refinement Simulation item in the job history window Joe Croep O esbrwtiod Tere Seccess Gate 1232550406917 Diase2Vensacreern 2009 01 21 2307 35 100 Show simulation results 123244 ae 2009 01 20 16 S1 41 100 2909 01 19 0076 38 100 009 01 15 22 52 46 100x 9009 01 15 22 5241 100 r i R09 01 15 22 52 18 100 1232030943423 Duse2Vewatcreern 1212071491777 Dune Vrtuslicreeren 1232023493773 Duse Vetualcreeren 7 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
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