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• Main Page
  | [https://bkslab.org The lab web page] || [[:Category:FAQ|FAQ]] || [[Feedback]] || [[Other tools]] || [[:Catego
  4 KB (487 words) - 20:36, 7 May 2024
• One page paper
  "http://zinc15.docking.org/observations.txt:zinc_id+substance.mwt+gene.name+gene.major_class_name+gene.sub_class_name+affinity?sort=zinc_id&count=all"
  362 bytes (55 words) - 04:24, 22 July 2015

Page text matches

• Erice2010:workshop5
  This is the SHARP-autoSHARP workshop page, run by Clemens Vonrhein, Erice 2010. [[Portal:Erice2010 | return to main workshop page]]
  262 bytes (35 words) - 20:17, 8 October 2012
• ZINC15:Endpoints
  | home || Landing page, query page || Provide navigation to other endpoints, search options
  566 bytes (71 words) - 17:55, 1 October 2015
• DOCK Blaster:Sample data
  Please see our data page [http://data.docking.org/ data.docking.org].
  97 bytes (15 words) - 18:09, 15 February 2014
• ZINC15:Variants
  '''http[s]://host/resource[.format[:columns][/variant][?page-view-controls | resource-constraints] | page=x || substance table || notes about substance table
  606 bytes (79 words) - 21:48, 16 September 2015
• DOCK Blaster:Results Browser
  === Page Header === === Detail Page ===
  547 bytes (71 words) - 20:02, 8 October 2012
• ZINC maintenance
  This page is just for John
  102 bytes (16 words) - 05:27, 14 February 2014
• DOCK Blaster:Input Troubleshooting
  troubleshooting page.
  70 bytes (7 words) - 20:02, 8 October 2012
• Disk Quotas
  Grant access on bet: (belongs on quotas page) update magdalena on work (belongs on quotas page)
  689 bytes (111 words) - 17:31, 17 August 2017
• Clinical trials curation
  This is the curator page for clinical trials curation. update subname set name=regexp_replace(name, ' *.inn.*$','') where name like '%[inn%';
  1 KB (238 words) - 18:53, 17 August 2017
• How to be someone
  This page collects references to articles about "how to be ..." a particular person.
  214 bytes (31 words) - 05:58, 9 May 2024
• Erice2010:Workshop3
  ...sit http://www.proteopedia.org''' and click on the green links on the main page.</big> ...f a 3D structure that feels incredibly intuitive to the person viewing the page.
  2 KB (371 words) - 20:17, 8 October 2012
• PubChem in ChEMBL
  I couldn't figure it out. When I typed the name of the project into ...he PubChem link at the bottom of the page and then scroll down the PubChem page, you will see the assay it relates to.
  2 KB (288 words) - 17:24, 23 February 2015
• Docker
  ===old page=== performed. Hopefully, Docker 1.0 and the above mentioned page might be
  2 KB (282 words) - 03:50, 29 August 2018
• DOCK Blaster:Tutorial 1
  a. Browse to the DOCK Blaster main page: You will get a confirmation page showing that the target has been looked up correctly at the PDB. To procee
  2 KB (302 words) - 02:22, 11 January 2019
• InChIs in ZINC15
  InChI and InChI key are now displayed on every molecule detail page, for instance You can search by InChI and InChIKey using the Search home page:
  1 KB (192 words) - 20:23, 8 December 2015
• Zinc2012paper
  We will update this page after the paper has been published.
  238 bytes (40 words) - 23:11, 4 January 2019
• Smiles update
  This is the internal instruction page for smiles update
  258 bytes (36 words) - 07:10, 13 March 2014
• Ldap admin
  ...user management system. LDAP. https://ds.ucsf.bkslab.org/ldapadmin/. This page is only relevant to sysadmins. home directory: /nfs/<name>/home
  926 bytes (153 words) - 21:41, 27 August 2018
• Tool-selector
  This page describes the tool selector. It is password protected, thus only for member * next takes you to next page. Also just edit URL to jump ahead to other pages.
  3 KB (461 words) - 19:46, 3 November 2016
• ZINC15:help
  ...esource]] in ZINC15 has an associated help page. Thus for substances, the page is [http://zinc15.docking.org/substances/help /substances/help]. Each /<resource>/help page is divided into six sections, which we take up in turn below. Please look
  3 KB (402 words) - 06:48, 10 October 2015
• Heather's notes
  ...Reload Page button got "we have no idea what we were asked to do" expected page to refresh (assume that this feature is not working yet) Typo - On Get Started page, last bullet - You may be one of those people, like me, who tries to do as
  2 KB (435 words) - 20:25, 8 October 2012
• General zinc15 curation
  update purchasability (belongs on curator page)
  236 bytes (31 words) - 17:32, 17 August 2017
• ZINC-22 news of Mar-22
  This page is for big changes to ZINC-22 during March 2022.
  193 bytes (29 words) - 15:29, 5 March 2022
• 2D to 3D
  If you know of more programs that do 2D to 3D, please amend this page.
  281 bytes (43 words) - 23:21, 11 March 2014
• ChemAxon
  ...ful to ChemAxon and the folks there for making it available to us. The web page is [http://chemaxon.com chemaxon.com].
  296 bytes (43 words) - 04:21, 3 June 2015
• DOCK Blaster:4100
  ...ave done before. For more information, please see the [[Target:CDK2]] wiki page OR please join the [http://docking.org/?q=node/12 cdk2 discussion forum].
  321 bytes (56 words) - 20:02, 8 October 2012
• Decoy:Problems
  This is the DUD/DUDE/decoy problem page, one of the [[:Category:Problems]] pages.
  220 bytes (33 words) - 15:00, 14 May 2014
• Contribute
  * Each page should ideally be categorized by at least one [[:Category:Article_type | ar * If a page is not appropriate for general readership, it should have one or more [[:Ca
  1 KB (200 words) - 18:54, 19 December 2018
• ZINC15:Formats
  '''http[s]://host/resource[.format[:columns][/variant][?page-view-controls | resource-constraints]
  472 bytes (58 words) - 20:56, 4 March 2015
• Rack Power (PDUs)
  This page will detail what PDUs are in which rack and how much Amperage they can hold
  295 bytes (44 words) - 21:15, 12 September 2023
• Zinc OICR
  This page documents the connections and data exchange between ZINC and OICR.
  513 bytes (78 words) - 20:50, 2 May 2024
• Get msms
  [http://mgltools.scripps.edu/packages/MSMS/ msms page]
  471 bytes (68 words) - 18:11, 2 May 2024
• CDK2
  This is the target page for CDK2.
  402 bytes (64 words) - 18:10, 8 October 2012
• Enzyme Function Initiative
  This in the main page for our participation in this project.
  440 bytes (58 words) - 17:42, 2 May 2024
• The 2014 migration
  ...e lab, or you use our cluster via ssh, big changes are afoot in 2014. This page describes what is happening, a tentative timeline, and answers some questio Please see the [[:Category:Cluster]] page for a summary.
  1 KB (212 words) - 14:20, 13 May 2014
• Tools18:about
  This is the about page for DOCK Blaster 18.
  352 bytes (55 words) - 23:28, 4 October 2018
• Stopping spam subscribes on mailman
  1) Go to mailing list pending administration page ...te('value') == '3') { input.checked = true; } else if (input.getAttribute('name').indexOf('ban-') === 0) { input.checked=true; } }
  670 bytes (97 words) - 21:54, 13 January 2016
• Delphi
  To understand (somewhat) how Delphi is used to score ligands, see this page on [[visualizing delphi]] grids.
  511 bytes (79 words) - 20:11, 8 October 2012
• Blaster Issues
  This page describes current problems with DOCK Blaster.
  442 bytes (63 words) - 23:37, 30 October 2012
• ZINC15:Getting started
  ...ces]] in ZINC15. The ZINC button (left) will bring you back to the welcome page. The four most popular resources are displayed next: Substances, Catalogs a ...g window. There is a many molecule search tool on the right side of this page.
  5 KB (842 words) - 03:49, 2 October 2015
• OCI:install client locally
  Following the instructions from this page
  864 bytes (140 words) - 23:39, 23 February 2022
• Mol2db2
  See the following page for information on the database formate: [[Mol2db2 Format 2]].
  455 bytes (64 words) - 15:46, 23 October 2014
• ZINC:Tutorials
  [[Category: EMPTY PAGE]]
  486 bytes (65 words) - 00:46, 5 January 2019
• Docking for experts
  This is the docking for experts main page. The goal of "docking for experts" is to be a comprehensive resource of eve
  516 bytes (63 words) - 05:12, 13 March 2014
• ZINC15:Query operators
  '''http[s]://host/resource[.format[:columns][/variant][?page-view-controls | resource-constraints]
  687 bytes (88 words) - 21:48, 16 September 2015
• How to install DOCK 3.8
  ...able DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program. See this page: [[How_to_compile_DOCK]]
  2 KB (274 words) - 04:52, 3 March 2023
• DOCK 3.6
  ...://shoichetlab.compbio.ucsf.edu/publications.php Shoichet Lab Publications Page] * See [[Dock Ligand Clustering]] page for more information
  2 KB (326 words) - 22:15, 2 January 2019
• ZINC:Command language
  catalog.name=<name> e.g. http://zinc.docking.org/results?catalog.name=:ChemBridge,Molport
  3 KB (433 words) - 21:34, 28 December 2018
• DOCK Blaster:CPU Time
  DOCK Blaster can take hours. This page will describe roughly how to figure out how long a run will take.
  326 bytes (45 words) - 20:02, 8 October 2012
• Workflow
  This is the workflow page.
  838 bytes (118 words) - 06:05, 13 March 2014
• DOCK Blaster:Job Management
  ...ed is checked in various ways to avoid failure later in the pipeline. This page describes the steps taken by our automated scripts, the messages you may re ...e submit, proceed to the Job Watcher. Otherwise, go back to the main input page.
  3 KB (449 words) - 20:02, 8 October 2012
• ZINC22:Timeline
  This is the timeline page for ZINC22.
  421 bytes (57 words) - 22:32, 14 December 2020
• Flexible docking code
  This is a page to document the old flexible docking / flexible water scripts and will hope
  635 bytes (110 words) - 03:39, 14 February 2014
• Public databases
  Some of these are free, some are commercial, and thus this page has been tagged in both categories.
  991 bytes (129 words) - 15:15, 14 February 2014
• Github
  This page describes how to use github, our [[version control]] system. This page is only relevant to [[:Category:Developer | software developers]]. see the following wiki page on how to generate a ssh key pair:
  3 KB (438 words) - 18:50, 27 August 2014
• Unpack-repack
  This is the page about unpack-repack for ZINC-22.
  602 bytes (95 words) - 21:29, 29 July 2021
• IPMI
  This page is about IPMI.
  583 bytes (68 words) - 15:24, 13 March 2014
• TLDR:bbfilter
  ...found on the chemistry commons (commons.docking.org) in the reactionClass page. http://commons.docking.org/reactionClass/
  786 bytes (121 words) - 19:42, 15 March 2023
• DUMM5
  &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
  709 bytes (91 words) - 20:11, 8 October 2012
• DOCK:Problems
  This is the UCSF DOCK problem page. There are other problem pages too:
  611 bytes (76 words) - 20:02, 8 October 2012
• Dock67
  This page describes the changes and novelties introduced in version 67 of the Shoiche
  713 bytes (113 words) - 23:10, 10 March 2014
• Dock development
  This page needs a lot of work. For now, this is how you check out DOCK 3.5.54 from th
  576 bytes (99 words) - 21:46, 10 January 2019
• Greatest hits
  This is a page about docking successes. I am just going to paste papers in here, with a vi
  704 bytes (101 words) - 04:38, 13 March 2014
• ZINC15:Properties
  '''http[s]://host/resource[.format[:columns][/variant][?page-view-controls | resource-constraints] ! table name !! Description !! Notes/Links
  914 bytes (121 words) - 21:49, 16 September 2015
• How to use Globus
  == ZINC Globus Endpoint Name == #On the left side of the page, click the "ENDPOINTS" button on the navigation bar.
  2 KB (338 words) - 00:34, 16 December 2022
• B. Comparing the interactions of different ligands with the same target
  ...earch''' at the top of the page. In the resulting '''Binding Site Analysis page''', type 100% in the '''Minimum Sequence Identity''' box and 2.5 in the ''' '''iii)''' In the Superposition Analysis page that comes up there is a lot of information about differences between the r
  3 KB (561 words) - 09:56, 13 March 2014
• ZINC15:Syntax
  ...ages and a machine-readable application programming interface (API). This page describes both. ! Name
  8 KB (1,085 words) - 01:01, 5 January 2019
• DUMM3
  ''Peter'': there is a page describing [[How to use the QB3 cluster|docking on the QB3 cluster]].<br> &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
  2 KB (333 words) - 20:11, 8 October 2012
• Testing zinc21
  This page describes testing zinc21 prior to full scale deployment.
  785 bytes (106 words) - 22:35, 1 July 2019
• Micromedex
  Then, click on mobileMicromedex (top of page)
  781 bytes (114 words) - 15:12, 14 February 2014
• Adverse
  main web page ->
  767 bytes (124 words) - 17:05, 23 March 2017
• There must be 5 ways to kick zinc
  5) Flush an individual cache page (note: the port and ? are required)
  730 bytes (118 words) - 17:40, 17 December 2015
• Dock my own molecules
  = In DOCK Blaster, select your subset on the "job watch" page =
  757 bytes (124 words) - 22:06, 4 January 2019
• Performing a Query on 22B Molecules
  ...rform the query on. Press "submit" and you will be redirected to the /jobs page, where you can see the current status of your query request. Once your quer From the index, navigate to /upload. On this page you can select a SMILES database to upload to the round table network. You
  2 KB (405 words) - 23:23, 17 April 2020
• Erice2010:workshop1
  * [http://www-cryst.bioc.cam.ac.uk/ Blundell Group home page] [[Portal:Erice2010 | return to main workshop page]]
  4 KB (562 words) - 20:17, 8 October 2012
• Pattern and reaction curation
  This is the pattern and reaction curation page.
  893 bytes (117 words) - 23:17, 1 March 2018
• Reactome integration
  ...t the small molecules currently released in Reactome, you can look at this page:
  1 KB (175 words) - 14:11, 6 September 2016
• Curating AMIS
  * 3. To click page number change pages until you can find the slices that has no image
  658 bytes (120 words) - 16:11, 27 July 2021
• Remote Procedure Calls
  ...cumenting them. Ask us if you are interested. Also check the [[ZINC api]] page.
  1 KB (181 words) - 13:37, 1 May 2014
• Choosing a subset
  These are subsets created by users, from the search results page, using the "create subsets" button. Some are also created as byproducts of ...eliberately kept the pull down menu on the DOCK Blaster "Calibration done" page simple. Just open ZINC in another browser window to understand the abbrevi
  3 KB (398 words) - 03:07, 14 February 2014
• Dockable metabolites libraries
  these are the ZINC 12 metabolites. The download links are on the page.
  1 KB (231 words) - 17:56, 22 June 2015
• DOCK 3.7 Development
  This page is for DOCK 3.7 developers. Back to [[DOCK 3.7]].
  1 KB (148 words) - 04:19, 1 October 2015
• WINC annotations
  ...ctivity having P-values better than 10^-10, which are accessible from this page. ...st a number we use to keep track of each annotation internally, and is the name of the SMILES file containing all the suggestions that you can get by click
  3 KB (487 words) - 04:37, 14 February 2014
• UCSF Strain Filtering
  *guys, any reason to keep this page? or just delete it*
  1,012 bytes (172 words) - 01:39, 15 December 2020
• Example of Disorder
  [http://blaster.docking.org/start.shtml start with a structure] page.
  943 bytes (144 words) - 16:12, 14 February 2014
• Zinc22 restart wynton
  This is a temporary page describing how to use DOCK 3.8 restartable on Wynton.
  985 bytes (161 words) - 05:46, 19 January 2021
• LoadingZINC15
  * 7. blog about it. tweet about it. update the backlog page.
  980 bytes (154 words) - 17:01, 22 June 2015
• ZINC15 todo
  http://band.desktop.ucsf.bkslab.org:8088/atccodes/L01A/genes.ldjson:name+major_class_name+sub_class_name http://band.desktop.ucsf.bkslab.org:8088/atccodes/L01B/genes.ldjson:name+major_class_name+sub_class_name
  2 KB (331 words) - 00:00, 29 July 2015
• DOCK on cygwin
  This page specifies how to install DOCK on Windows OS.
  1 KB (197 words) - 23:38, 22 July 2014
• Openeye python libraries
  See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br /> .../python/quickstart-python/linuxosx.html#installing-openeye-python-toolkits page on OpenEye website] explaining different ways to set it up.
  3 KB (454 words) - 23:32, 13 March 2019
• ChEMBL API
  ...es we have added some example Perl and Python scripts to our documentation page. We hope that these scripts will help you in your efforts to interact with
  1 KB (237 words) - 06:46, 13 March 2014
• Erice2010:workshop7
  [[Portal:Erice2010 | return to main workshop page]]
  1 KB (173 words) - 20:17, 8 October 2012
• Tomcat Installation on CentOS 6
  From here you can click the button Manager App to access the manager page, or simply go to The user name is admin. The password is the usual password.
  3 KB (489 words) - 02:22, 10 July 2020
• Legacy IDs in ZINC22
  BKS cluster members can follow the instructions on this page: [[Search zinc22.py]] to look up ZINC IDs and vendor codes outside of cartb
  1 KB (202 words) - 18:09, 30 June 2022
• Erice2010:workshop11
  [[Portal:Erice2010 | return to main workshop page]]
  1 KB (206 words) - 20:17, 8 October 2012
• ZINC15:What's New
  See our examples page for examples of the new questions that may be asked. [[ZINC15:examples]].
  1 KB (216 words) - 23:07, 4 January 2019
• AWS:Cleanup
  This page is about how to clean up your AWS account after you have finished docking.
  1 KB (215 words) - 21:29, 14 September 2022
• XML RPC Services
  ...MLRPC) services. These are based on supported [[XML RPC Procedures]]. This page is a crib sheet on how to use these services. Note that the use of docking.
  2 KB (247 words) - 00:52, 11 March 2014
• Welcome group members
  Welcome to the lab! This page organizes topics of interest to group members, our collaborators and anyone ...]s for an account on the cluster, and a workstation. Tell us what account name you prefer.
  4 KB (629 words) - 21:06, 30 December 2020
• A. Substructure searching in Relibase
  ...will automatically be transferred to the '''Substructure Search Results''' page. The search will result in over 450 hits, indicating that the fragment is p ...the ‘tree’ can be expanded by clicking on the + sign next to the structure name. Asp189 is an important anchor in the S1 pocket of serine proteases.
  4 KB (637 words) - 09:55, 13 March 2014