Search results

Jump to navigation Jump to search

Page title matches

  • 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
  • Loading ZINC12
    ...s the internal page for loading ZINC. If you are not a ZINC curator, this page will probably not be interesting.
    3 KB (408 words) - 23:23, 4 January 2019
  • Preparing dockfiles using TLDR
    This page describes how to use TLDR:blaster2.0 service to create dockfiles for large
    1 KB (177 words) - 18:43, 9 August 2022
  • DOCK3.7 INDOCK
    ...le, alongside a sample file. blastermaster.py described on the [[Dock3.7]] page writes an INDOCK file for you, which you can modify.
    5 KB (537 words) - 18:10, 15 February 2014
  • Ssh tunnel (Trent's way)
    This assumes that you have already created the a key pair. See this page [[How to generate ssh keys securely]]. The public key has been put onto por ...calhost that points to gimel and will connect through epsilon (a different name for portal).
    1 KB (246 words) - 18:16, 18 August 2022
  • ZINC-22 news of Jan-22
    ...are some things you need to be aware of. These are described in this wiki page: [[ZINC-22 Clean Up in Jan 2022]]
    1 KB (227 words) - 17:10, 2 February 2022
  • DOCK Blaster:Tutorial 8
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    6 KB (878 words) - 03:24, 12 March 2014
  • DOCK Blaster:Prepare Input
    ...e additional information about actives and inactives for this target. This page provides a quick overview of preparing input files for docking. It also ref and the [[DOCK Blaster]] main page.
    6 KB (944 words) - 20:02, 8 October 2012
  • Protein Target Preparation
    ...d consult the changed version written for you, or take a finer look at the page on the DOCK3.7 INDOCK file.
    2 KB (264 words) - 16:57, 28 August 2019
  • DOCK Blaster:Tutorial 4
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 2
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 5
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 6
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    10 KB (1,582 words) - 03:24, 12 March 2014
  • DOCK Blaster:Tutorial 7
    * P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selec * P2.1. Go to the [http://blaster.docking.org | DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml | Queue A Job] from the
    10 KB (1,582 words) - 03:24, 12 March 2014
  • User Reported Problems
    ...ne to address the issue and leave it here for a month. We'll make another page with problems that were resolved (soonish). ...jobs running. Upon checking n-1-113, there was no active process with her name yet the SGE queue indicated she had an active job. This problem only seeme
    1 KB (217 words) - 18:31, 26 February 2018
  • ZINC subsets
    Neutral-fragments (#17) are what the name suggests: uncharged fragments. Why would you want this? Charged compounds o ...lity to create small subsets. You can do this via the ZINC results browser page after a search by clicking on "create subset". Another way, if you have the
    7 KB (1,114 words) - 05:28, 14 February 2014
  • AWS:Merge and download results
    ...w key pair for your instance. Use RSA encryption and give it a descriptive name, making sure to save the .pem or .ppk file somewhere you will remember it. Now launch your instance, this will bring you to a page showing your instance's ID. Click on that ID to view the details of your in
    6 KB (897 words) - 21:30, 14 September 2022
  • Anchor and Grow
    ...torsion angle positions reside in an editable file (see flex_drive.tbl on page 111) which is identified with the flex_drive_file parameter. Internal clash
    2 KB (260 words) - 00:12, 11 March 2014
  • Set up a database server
    This page describes how to set up a database server.
    2 KB (215 words) - 22:03, 9 March 2016
  • DUMM2
    &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
    1 KB (208 words) - 20:11, 8 October 2012
  • Cluster 4
    Cluster 4 is our self-centric name for the SciNet cluster in Canada. (1.1) go to the following page and click Register:
    2 KB (271 words) - 01:22, 31 March 2014
  • AWS:Upload docking files to aws
    Select “create bucket” in the top right. Give your bucket a name and confirm creation of the bucket When you click on a file or directory, it will bring you to a page either describing the details of the file, or listing the contents of the d
    1 KB (263 words) - 18:58, 9 August 2022
  • DUMM4
    &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
    2 KB (248 words) - 20:11, 8 October 2012
  • Build ChEMBL for SEA
    ...blic rename to <schema_name>; # <schema_name> is going to match the schema name setup in script 0_load_chembl_database.R ...ase it timing out, you could specify the page where it timed out by adding page=<page_num>
    6 KB (922 words) - 21:19, 22 June 2023
  • ZINC22:Checkout
    This page describes checking out ZINC22 SMILES tranches for 3D building.
    2 KB (342 words) - 19:12, 28 January 2021
  • Configuring an OpenSSH Server
    For fail2ban install and configuration go to page For logwatch install and configuration go to page
    7 KB (954 words) - 22:05, 27 June 2016
  • DOCK Blaster:Broken molecules
    2. You can write a wiki page to document the problem you see
    2 KB (318 words) - 20:02, 8 October 2012
  • ZINC
    ''Click [[:Category:ZINC|ZINC Category page]] for documentations.'' Please see the [http://zinc15.docking.org/catalogs catalogs] page. If there is a catalog you would like to see loaded, please write to databa
    11 KB (1,604 words) - 23:52, 10 January 2019
  • Mol2db
    The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not
    2 KB (347 words) - 23:21, 4 January 2019
  • DUD
    We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful fe
    2 KB (284 words) - 20:44, 3 January 2019
  • Filtering Rules
    ...filtered-out compound is justified with a reason, available via the vendor page. Every compound in every supplier catalog we load has one of four fates:
    2 KB (305 words) - 17:57, 18 March 2014
  • ZINC:FAQ
    Every subset page and every vendor page has a special link for downloading the subset on Windows and on Unix, which
    5 KB (757 words) - 15:42, 11 March 2014
  • DUMM6
    &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
    2 KB (270 words) - 20:11, 8 October 2012
  • Erice2010:Workshop9
    [[Portal:Erice2010 | return to main workshop page]]
    2 KB (317 words) - 20:17, 8 October 2012
  • OCI:Set up account
    An Oracle OCI account is also required, with payment attached. (payment page goes here) ...et key and access key are, follow this tutorial: (my secret access key web page)
    8 KB (1,318 words) - 18:35, 22 March 2023
  • Oracle scraps
    ...ults (returned block size, provides fast results as first 100 returned for page, then can continue searching while visualization calls present the webpage) Family clustering on results page. eg instead of showing 25 stereoisomers, show a non-stereo compound and giv
    5 KB (681 words) - 17:01, 18 March 2014
  • ZINC-22:Select chemical space for docking
    This page allows you to select any subset of chemical space you would like. There are
    2 KB (314 words) - 18:52, 9 August 2022
  • How to link to ZINC
    http://zinc.docking.org/results?page.format=zinc&filter.purchasable=purchasable&zinc.id=$ZINC_ID wget -qO- http://zinc.docking.org/results?page.format=zinc&filter.purchasable=purchasable&zinc.id=53
    4 KB (542 words) - 00:47, 10 January 2019
  • So you want to set up a lab
    This page describes setting up a full computational pharmacology research lab. We des
    2 KB (340 words) - 19:38, 10 January 2019
  • Api15
    ...cking.org api15.docking.org]. Requests may be invoked starting from a web page, or by using curl or wget. As much as possible, each operation is atomic, ...tion, and action and arguments are defined in the relevant section of this page.
    6 KB (882 words) - 00:14, 2 October 2015
  • Python DOCK3.8
    ...script with a special requirement, please message me so I can update this page and make the python version widely available. My email is ben@tingle.org.
    2 KB (359 words) - 19:02, 28 May 2021
  • ZINC15:Levels
    ...king.org zinc15.docking.org] and clicking the mouse and/or typing into web page fields. No editing of the URL is necessary. Free and public, no special acc
    2 KB (307 words) - 18:03, 10 January 2019
  • DOCK Blaster:FAQ
    * [[Problems]] page for a general overview of all problems. * [[Bugs]] page for information about bugs. Please report bugs to support at docking.org.
    9 KB (1,448 words) - 22:06, 5 April 2013
  • ZINC12
    [http://zinc.docking.org/browse/catalogs/ Subsets->Catalog] page. If there is a catalog you would like to see loaded, please write to databa * [http://facebook.com/zincdb ZINC Facebook page contains links to sites that use ZINC]
    8 KB (1,258 words) - 23:54, 4 January 2019
  • Prepare a receptor with a cofactor for docking
    This page is written by Trent E. Balius (FNLCR) on March 28, 2020.
    3 KB (437 words) - 23:37, 28 March 2020
  • Covid19
    Single landing page for lab procedures affected by the campus closure due to Covid19.
    2 KB (355 words) - 16:37, 17 March 2020
  • Omega.py
    2) Edit and save omega.parm (using the same name) in your favorite editor. An example of omega.parm is shown at the bottom of this page. Settings you may want to consider changing are:
    3 KB (389 words) - 04:08, 14 February 2014
  • DOCK Blaster:Timings
    ...ready, all you are doing is loading pages and browsing results. Loading a page of 500 results into the browser could take a minute, but will often be less
    3 KB (444 words) - 05:22, 13 March 2014
  • Dock Sampling
    ...ut it can be broken down to two main processes: scoring and sampling. This page is about sampling (in DOCK). ...actually sampled in the docking process. This is what is described on this page.
    8 KB (1,222 words) - 16:11, 14 February 2014
  • NCI Platted
    ...re NNNN is the NSC number you are seeking. That will lead you to a result page that has menu picks for related structures.
    3 KB (537 words) - 16:07, 2 July 2014
  • ZINC:Problems
    This is the ZINC problems page, which describes all the problems specific to [[ZINC]].
    3 KB (428 words) - 21:06, 4 October 2016
  • ZINC:Errata
    ...MILES strings, these match the 2D depictions you see on the search results page (not suprising, really, as I imagine that the 2D depictions are generated d
    3 KB (462 words) - 05:35, 22 February 2017
  • To resize a virtual drive
    0) Read man page virsh shutdown <vm-name>
    2 KB (336 words) - 18:49, 5 October 2016
  • Loading And Creating ZINC Partitions Automatically
    In this wiki page I will describe the journey of
    3 KB (499 words) - 04:07, 29 May 2020
  • Irwin:workshop1
    [[Portal:Erice2010 | return to main workshop page]]
    4 KB (578 words) - 20:27, 8 October 2012
  • 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
  • ZINC12 mechanics
    $userDB->store('get_something_cool', "SELECT name FROM users WHERE coolness=$1"); echo "{$person['name']}, ";
    3 KB (496 words) - 22:39, 4 January 2019
  • PuppetTricks
    This page is a collection of tricks and tips for using Puppet to administer systems. ...', and '''foreman''' all refer to (at the time of writing this) alpha. The name '''client''' refers to any machine that is maintained by puppet.
    8 KB (1,165 words) - 00:45, 28 April 2022
  • DOCK 3.8:How to build a release
    This page describes the formal definition of a release of the [https://dock.compbio.u
    3 KB (491 words) - 21:46, 22 February 2024
  • Excipients
    -> copy over the additive list from this page (https://www.fda.gov/Food/IngredientsPackagingLabeling/FoodAdditivesIngredi
    4 KB (480 words) - 18:47, 24 July 2017
  • Continuous curation
    We continually curate ZINC. This page describes the actions taken (briefly) and the current status, with date.
    3 KB (406 words) - 17:23, 15 November 2016
  • Erice2010:workshop2
    [[Portal:Erice2010 | return to main workshop page]]
    4 KB (580 words) - 20:17, 8 October 2012
  • Building The 3D Pipeline ZINC22
    See this wiki page for how to do this: [[Repackaging_DB2_DOCK38]] ...e to be built. This file should contain only two columns of data: (SMILES, NAME) with no header.
    10 KB (1,616 words) - 18:11, 9 March 2023
  • Understanding MakeDOCK, which automates sphere and grid generation
    To learn how to create and run a docking job, see the [[SGE Cluster Docking]] page.
    3 KB (488 words) - 02:43, 13 March 2014
  • Switch-5-1
    ...hernet cable to my laptop, I was able to access the switch's configuration page with a web browser by putting the switch's default IP address 192.168.0.239
    4 KB (592 words) - 03:44, 13 July 2019
  • How to check RAM details
    Page will be interest those who want to find information regarding what RAM exis # The manufacturer name sometimes shows up as an actual company name (ie Samsung/Crucial/Kingston) but sometimes it comes out as gibberish like
    3 KB (448 words) - 20:54, 26 March 2018
  • DOCK 3.7 tart
    You may want to visualize your modified potential maps. See the following page on how to do this with pymol:
    4 KB (579 words) - 18:04, 6 June 2018
  • Flexible Docking
    ...or the SI of the Fischer, Coleman et al paper on the Citations for DOCK3.7 page.
    3 KB (510 words) - 21:37, 13 February 2014
  • AWS:Submit docking job
    You'll be greeted by a prompt to enter the full name (or identifier) of your desired environment. If you just ran through the qu [ What is the full name ($name-$region) of the environment to submit to? ]: dockenv-us-east-1</nowiki>
    8 KB (1,398 words) - 22:11, 11 October 2022
  • PBSA Score
    ...the tool kit, licensing, and other OpenEye products, go to the OpenEye web page at www.eyesopen.com **** Name of receptor file.
    4 KB (513 words) - 04:01, 14 February 2014
  • ZINC15:current limitations
    ...vendors need updating. If you tell us what they are (via discus, bottom of page) we will update them more quickly.
    3 KB (550 words) - 14:52, 10 October 2015
  • Omega.parm
    2) Edit and save omega.parm (using the same name) in your favorite editor. An example of omega.parm is shown at the bottom of this page. Settings you may want to consider changing are:
    4 KB (557 words) - 04:10, 14 February 2014
  • Erice2010:workshop6
    [[Portal:Erice2010 | return to main workshop page]]
    4 KB (549 words) - 20:17, 8 October 2012
  • Analyzing DOCK 3.7 Results
    Note: this page was adapted from https://sites.google.com/site/dock37wiki/home/analyzing-do
    3 KB (601 words) - 21:22, 13 February 2014
  • DOCK Blaster:Progress Bar
    This is the page you see immediately after pressing the "DOCK" button. Your data are uploade
    4 KB (686 words) - 20:02, 8 October 2012
  • How to generate ssh keys securely
    For all the following examples ''you'' is the user’s name that needs the ssh key and anything italicized is an example or comment (ju Create a folder “ssh-stuff” (or whatever name makes sense to you to store you ssh keys in) in Computer -> Local Disk (C:)
    5 KB (839 words) - 17:45, 20 September 2016
  • Smallworld and Arthor Databases
    This page details the databases on Smallworld and Arthor.
    5 KB (755 words) - 19:27, 13 June 2023
  • Upload Wizard
    Fields are the column name of the catalog: Optional: Price, Compound Name, CAS
    4 KB (639 words) - 18:01, 28 October 2019
  • DUMM1
    &rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]
    4 KB (698 words) - 20:11, 8 October 2012
  • Cluster Narrative
    ...ational pharmacology and computer aided drug discovery is a big deal. This page is part of a series of articles called [[So you want to set up a lab]]. He
    4 KB (692 words) - 18:25, 22 September 2014
  • DUDE
    This is the Wiki Page for '''DUD-E''' or (we like to call "DUDE"), a '''D'''irectory of '''U'''se This page contains documentation, FAQ, and may be used for posting errors and omissio
    12 KB (1,955 words) - 20:35, 4 January 2019
  • ZINC15:examples:public
    ...king.org/activities.txt:gene.name?activities.affinitynm:ge=8&distinct=gene.name&count=all http://zincapi.ucsf.bkslab.org/v1/activities/txt:target.gene.name,substance.smiles,substance.zinc_id,substance.purchasability/activity.affini
    18 KB (2,725 words) - 21:41, 29 October 2019
  • Creating Maps on SmallWorld
    Note that +19 is the lowest priority possible. Consult the man page for more information. Here the 3 represents idle. Consult the man page for other options such as -c 2 which has different priority levels for best
    10 KB (1,734 words) - 00:11, 9 January 2020
  • ZINC22:Numbering
    This page maps ZINC22 numbering. ZINC numbers are built as follows:
    3 KB (390 words) - 20:57, 28 September 2022
  • Interactive ligands visualizer
    ...to run the visualizer directly from smiles and fingerprints, see bottom of page. activity_name = "Emax" # The text name of the activity (in this case, Emax)
    5 KB (855 words) - 23:54, 27 January 2023
  • Clinical Trials
    ...an search by the treatment type and trial phase from their advanced search page: ...nfo: CTI (Clinical Trials Insight) published by ADIS ( http://www.adis.com/page.asp?ObjectID=26); and TrialTrove published by CiteLine (http://www.citeline
    5 KB (823 words) - 02:40, 13 March 2014
  • Andrii's notes on SynthI
    Parent page: [[SynthI]]
    5 KB (729 words) - 19:40, 28 March 2022
  • ChEMBL errata
    This is a page to keep track of errata we've found with the ChEMBL database at [https://ww
    5 KB (737 words) - 14:46, 21 March 2014
  • Installing oracle
    :Required packages installed as per page :/etc/hosts configured to have fully resolved name:
    5 KB (754 words) - 18:33, 12 March 2014
  • Plop
    This page describes simple protocols for receptor/active site and ligand minimization
    5 KB (825 words) - 12:37, 21 March 2014
  • Tomcat Installation
    As of the writing of this page, the latest version of Tomcat 9 is 9.0.30
    5 KB (768 words) - 22:07, 22 January 2020
  • GPU DOCK
    ```THIS PAGE IS CURRENTLY WIP``` ...es, single thread model that subdock currently uses. See further down this page for more details).
    20 KB (3,437 words) - 20:50, 22 April 2023
  • Dockenv Scripts
    snap.csh - take picture using indycam and put on web page
    5 KB (845 words) - 17:25, 2 May 2024
  • Assaying Compound Activity
    ...g it tested either in house or sending it out somewhere to be tested. This page details some of the common tasks and considerations in this process. Note, ** Provide the courier (e.g. FedEx) with the address and full name and telephone number of the person who will receive it.
    5 KB (880 words) - 21:37, 24 October 2014
  • How to use Arthor API
    ${db_name} Required path variable, the database name is specified in the URL path as ${db_name}. For one of the databases above, ...parameter hasMore indicates whether there are more results. When the first page for a query is requested a background counter is spun up to count the total
    6 KB (901 words) - 20:50, 16 February 2023
  • Cluster 0
    This page is about our legacy cluster at [[Mission Bay]]. Most users should use [[Cl
    6 KB (769 words) - 00:10, 9 April 2017
  • How to Migrate a Virtual Machine
    This page shall describe how to transfer a virtual machine from one hypervisor to ano Id Name State
    6 KB (939 words) - 18:24, 23 May 2017
  • DOCK 3.7 tutorial based on Webinar 2017/06/28
    ...d "ligands_12_from_chembl.smi" with the smiles in the first column and the name in the second column. For more information see the page: [[Ligand_preparation_-_20170424]]
    7 KB (931 words) - 15:31, 3 October 2017
  • DOCK 3.7 tutorial (Anat)
    ...ke sure that there are no ^M in the smiles input file - use dos2unix [file name] command remove them. See the this page: [[Trent_scripts]]
    6 KB (1,016 words) - 16:46, 19 August 2020
  • Dock3.7
    db2end-prefix.py name To build dockable name-XXXXXX.db2.gz files.
    6 KB (1,081 words) - 22:28, 12 June 2017
  • DOCK 3.7 2018/06/05 abl1 Tutorial
    #page=requests.get(url) page = webfile.read()
    27 KB (4,088 words) - 21:04, 19 October 2023
  • Erice2010:workshop8
    [[Portal:Erice2010 | return to main workshop page]]
    6 KB (874 words) - 20:17, 8 October 2012
  • DB2 File Format
    This page explains the DB2 file format used in DOCK37. A NUM NAME TYPEX DT CO +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
    7 KB (1,153 words) - 21:38, 19 April 2016
  • How To Load New ZINC Databases
    the name of the machine you are running this script on check batch_logs/<step name>_<job id>_<array id>.out for the log output of various jobs
    7 KB (1,168 words) - 18:50, 8 September 2021
  • DOCK 3.7 2015/04/15 abl1 Tutorial
    #page=requests.get(url) page = webfile.read()
    28 KB (4,315 words) - 21:05, 19 October 2023
  • DOCK:FAQ
    ...in) binding site. For more information, please see [[:Category:DOCK | DOCK page]]. ...the configuration file, dock6/install/config.h; LEX should be assigned the name of your lexical analyzer generator.
    7 KB (1,087 words) - 00:29, 11 January 2019
  • Renewing Puppet Certificates
    /etc/httpd/conf.d/25-puppet.conf (tells you what certificate name that the puppetmaster uses) ...d because certname in [master] section of /etc/puppet/puppet.conf has this name)
    18 KB (2,894 words) - 20:48, 10 May 2024
  • AWS:Set up account
    ...un before, you may see a bunch of errors along the lines of: "Service role name <blank> has been taken in this account". Don't worry about these, they don' ...obs. If you try to create an environment that already exists with the same name, the script will update the existing environment instead of creating a new
    8 KB (1,333 words) - 20:38, 19 October 2022
  • Server Room Machines
    ...servers that we have on our cluster. Additionally, we'll try to keep this page updated with the compatible RAM for each machine (info will be taken from m
    6 KB (940 words) - 00:27, 12 January 2019
  • Mol2db2 Format 2
    This page is a wishlist for features that would be nice for a new version of the flex A NUM NAME TYPEX DT CO +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
    7 KB (1,289 words) - 15:44, 23 October 2014
  • Slurm Installation Guide
    This page will show you how to setup and configure a Slurm queueing system.
    8 KB (1,109 words) - 20:27, 22 March 2024
  • SmallWorld Documentation for Future Developer
    Name=Atom Alignment Name=SMARTS Alignment
    12 KB (1,637 words) - 23:38, 1 May 2024
  • Membrane Modeling
    ...oteins/ and find your protein. Copy residue numbers from the bottom of the page to the field <code>Transmembrane atoms...</code>. The format is as follows: alter shell, name='C'
    23 KB (3,565 words) - 21:36, 31 May 2023
  • Set up a Server
    This page described how to install CentOS and setup/troubleshooting puppet 2. Change '''Host name''' at the bottom
    11 KB (1,504 words) - 03:03, 8 July 2022
  • Protein Target Preparation Updated
    where you have "ATOM", atom number, atom name, residue name, residue number, x coordinate, y coordinate, z coordinate, atomic radius, a ...heres, e.g. when parameter scanning, spheres can be included with the atom name as "X" (different from "C" as in the low dielectric spheres), as shown belo
    16 KB (2,467 words) - 18:59, 10 October 2019
  • Tutorial on running DOCK3.7 with GIST
    You can download other databases from the autodude web page: ...ript gets poses for top scoring molecules and produces poses.mol2 (default name)
    18 KB (2,525 words) - 01:31, 16 November 2017
  • Schrodinger
    Machine Name: nis.compbio.ucsf.edu Machine Name: bet2.cluster.ucsf.bkslab.org
    15 KB (2,301 words) - 19:07, 18 March 2024
  • How to dock in DOCK3.8
    Related page: Docking Analysis with DOCK 3.8 ...have SHRTCACHE be set to the value of another environment variable, whose name is the value of SHRTCACHE_USE_ENV. This is useful for example if the schedu
    16 KB (2,599 words) - 22:28, 1 December 2022
  • Ligand Flexibility
    file (see flex_drive.tbl on page 111) which is identified with the ...le specific anchor (e.g scaffold with known bonding pose), specify an atom name and its corresponding atom number in the chosen fragment (e.g. if atom numb
    18 KB (2,718 words) - 23:58, 23 March 2016
Retrieved from "http://wiki.docking.org/index.php?title=Special:Search"