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  • New it team members
    * Do the infamous tutorial
    926 bytes (144 words) - 19:25, 19 March 2020
  • AWS:Set up account
    * Tutorial 1 AWS:Set up account THIS TUTORIAL * Tutorial 2: [[AWS:Upload files for docking]]
    8 KB (1,333 words) - 20:38, 19 October 2022
  • OCI:Set up account
    * Tutorial 1 OCI:Set up account THIS TUTORIAL * Tutorial 2: [[OCI:Upload files for docking]]
    8 KB (1,318 words) - 18:35, 22 March 2023
  • Drugs
    [[Category:Tutorial]]
    1 KB (220 words) - 03:50, 23 July 2015
  • How to install and configure JupyterHub
    This tutorial shows how to install and configure JupyterHub on Centos 7.
    1 KB (224 words) - 23:51, 16 July 2018
  • Using thin spheres in DOCK3.7
    ...ow small your radius is. You can check your protein preparation using this tutorial: ==Tutorial for using Thin Spheres in DOCK 3.7.1rc1==
    6 KB (852 words) - 12:41, 4 September 2019
  • ECFP4 Best First Clustering
    Follow the tutorial [[Large-scale SMILES Requesting and Fingerprints Converting]] to get the sm
    1 KB (199 words) - 15:51, 19 September 2017
  • Chemical reactions
    [[Category:Tutorial]]
    1 KB (179 words) - 04:21, 1 October 2015
  • DOCK Blaster:Tutorial 8
    ...to Mineralocorticoid receptor''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    6 KB (878 words) - 03:24, 12 March 2014
  • Erice2010:workshop2
    ...d from SIRAS phasing using Buccaneer, and examining the model in Coot. The tutorial will also cover phase improvement using DM and simple refinement using Refm http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/index.html
    4 KB (580 words) - 20:17, 8 October 2012
  • Interacting with Chemaxon dataset
    ...ontend can be used for viewing and modifying the aggregator database. This tutorial demonstrates how to use JCman UI from the local machine.
    1 KB (158 words) - 18:05, 15 February 2014
  • Analyze ligand geometries using the Cambridge Structural Database (CSD)
    ...out single rotatable bonds is one of the most common uses of the CSD. This tutorial illustrates how '''Mogul''', part of the CSD software can be used to rapidl
    1 KB (180 words) - 23:16, 21 May 2019
  • More cool zinc15 tricks
    Here are questions you can ask. Ideally, work these into a tutorial of some kind:
    2 KB (325 words) - 00:11, 1 February 2017
  • Category:Tutorials
    Here is a list of nerdy topics that have not yet had the tutorial tag added. hint hint.
    109 members (1 subcategory, 0 files) - 19:57, 3 August 2018
  • AWS:Submit docking job
    * Tutorial 1: [[AWS:Set up account]] * Tutorial 2: [[AWS:Upload files for docking]]
    8 KB (1,398 words) - 22:11, 11 October 2022
  • March2019 protocol
    Here is the tutorial for the setup script for DOCK3
    1 KB (231 words) - 02:11, 6 April 2019
  • DOCK 3.7 2016/09/16 abl1 Tutorial(building)
    ...15 abl1 Tutorial. Former one works well and is very simple and clear. This tutorial mentions some updates in job submissions.
    7 KB (1,019 words) - 00:16, 18 September 2016
  • Visualizing delphi
    Tutorial on visualizing [[Delphi]] and understanding electrostatic scoring in [[DOCK
    1 KB (236 words) - 18:50, 15 February 2014
  • DOCKovalent cysteine inhibitor design tutorial
    This tutorial is for designing linkers for a covalent inhibitor and is supplement the wor ...are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial
    9 KB (1,113 words) - 22:23, 20 March 2023
  • DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)
    ...abl1 Tutorial]]. Former one works well and is very simple and clear. This tutorial mentions some updates in job submissions.
    7 KB (1,063 words) - 01:59, 19 September 2016
  • DOCK Blaster:Tutorial 4
    ...hihydrofolate Reductase (DHFR)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 2
    ...hihydrofolate Reductase (DHFR)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 5
    ...hihydrofolate Reductase (DHFR)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    10 KB (1,582 words) - 03:23, 12 March 2014
  • DOCK Blaster:Tutorial 6
    ...hihydrofolate Reductase (DHFR)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    10 KB (1,582 words) - 03:24, 12 March 2014
  • DOCK Blaster:Tutorial 7
    ...hihydrofolate Reductase (DHFR)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]]. This tutorial will show you how to retrospectively dock a crystallographically observed l
    10 KB (1,582 words) - 03:24, 12 March 2014
  • DOCK 3.7 2014/09/25 FXa Tutorial
    The focus of this tutorial is to perform a retrospective enrichment calculations and a test virtual sc == This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1. ==
    9 KB (1,429 words) - 23:37, 26 April 2016
  • SVN
    ...nbook.red-bean.com/nightly/en/svn.branchmerge.html Chapter 4, Official SVN tutorial] ...ve tutorial, see the [http://svnbook.red-bean.com/nightly/en/ Official SVN tutorial]
    7 KB (1,204 words) - 13:31, 23 April 2014
  • HEI
    ...rgy intermediate forms is described in a [[How to generate an HEI database|tutorial]].
    2 KB (252 words) - 15:22, 11 March 2014
  • Large-scale SMILES requesting
    This tutorial is for requesting a large number of SMILES for docking results from ZINC se
    3 KB (369 words) - 23:01, 18 September 2017
  • Large-scale SMILES Requesting and Fingerprints Converting
    This tutorial is for requesting a large number of SMILES for docking results from ZINC se
    3 KB (375 words) - 01:34, 19 September 2017
  • DOCKovalent lysine inhibitor design tutorial
    This tutorial is for designing linkers for a covalent inhibitor and is supplement the wor ...are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial
    7 KB (903 words) - 16:52, 11 April 2019
  • DOCKovalent linker design tutorial
    This tutorial is for designing linkers for a covalent inhibitor and is supplement the wor ...are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial
    7 KB (903 words) - 20:08, 18 June 2018
  • DOCKovalent linker design tutoral
    This tutorial is for designing linkers for a covalent inhibitor and is supplement the wor ...are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial
    7 KB (903 words) - 00:21, 6 April 2018
  • DOCKovalent lysine inihibitor design tutorial
    This tutorial is for designing linkers for a covalent inhibitor and is supplement the wor ...are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial
    7 KB (905 words) - 22:22, 20 March 2023
  • Removing Spheres (The Chase Method)
    ...you have run this script, you can visualize your spheres by following this tutorial:
    2 KB (386 words) - 20:17, 27 May 2020
  • ZINC-22:Select chemical space for docking
    This tutorial describes how to use CartBlanche22.docking.org to select chemical space for
    2 KB (314 words) - 18:52, 9 August 2022
  • Filtering ligands for novelty
    ...s for the knowns and the clusterheads that were calculated in the previous tutorial: [http://wiki.bkslab.org/index.php/How_to_process_results_from_a_large-scal
    3 KB (480 words) - 18:49, 15 March 2019
  • Chimera Tutorial (AMPC)
    Characterizing the β-lactamase binding site Chimera tutorial
    2 KB (283 words) - 18:12, 9 January 2017
  • Heather's notes
    Tutorial on how to prepare files for Dock Blaster using Chimera (it uses snapshot 23
    2 KB (435 words) - 20:25, 8 October 2012
  • ViewDock
    ...s a [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html tutorial] on the Chimera web pages.
    8 KB (521 words) - 16:58, 16 April 2020
  • Particle Shape Calculator for CCDC/Mercury
    This tutorial will introduce you to the morphology calculation features included For the purposes of this tutorial, we will keep the default options. These
    7 KB (1,199 words) - 21:25, 23 May 2023
  • DOCK 3.8
    How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. [[AWS:Set up account]]
    3 KB (413 words) - 17:06, 8 April 2023
  • How to process results from a large-scale docking
    This tutorial uses the DOCK3.7.1rc1.
    3 KB (522 words) - 22:39, 26 March 2019
  • Tomcat Installation on CentOS 6
    Follow the steps on this tutorial https://www.itzgeek.com/how-tos/linux/centos-how-tos/install-apache-tomcat-
    3 KB (489 words) - 02:22, 10 July 2020
  • Ligand File Input
    file for the ligand (see [[Structure Preparation Tutorial]])
    4 KB (576 words) - 23:28, 23 March 2016
  • How to do parallel search of smi files on the cluster
    This tutorial shows how to do parallel search of smi files on the cluster. The files and
    4 KB (536 words) - 18:02, 19 July 2018
  • Ligand File I/O
    ...techamber to prepare a MOL2 file for the ligand (see Structure Preparation Tutorial) or various other visualization packages. During the docking procedure, lig
    5 KB (691 words) - 17:48, 15 February 2014
  • Tutorial on running DOCK3.7 with GIST
    Tutorial by Trent Balius (2017/01/30). This tutorial assumes that you have already completed the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]].
    18 KB (2,525 words) - 01:31, 16 November 2017
  • Install operating system
    ...tion systems, such as kerberos, are fine, but are beyond the scope of this tutorial.
    3 KB (532 words) - 18:32, 22 September 2014
  • How to do parameter scanning
    Use the tutorial above instead. Or use this link to run blastermaster manually:
    6 KB (775 words) - 20:04, 21 September 2021
  • Setting Up An Automatic SSH Tunnel To Epsilon
    ...w now, which will minimize it to your notifications bar (on windows). This tutorial shows how to set up a Bitvise client, but these steps can also be applied t
    4 KB (720 words) - 21:37, 28 March 2020
  • Category:SEA
    * [[Basic Tutorial]]
    9 members (1 subcategory, 0 files) - 23:03, 25 July 2022
  • AWS DOCK Environment Setup Advanced Usage
    If you followed the tutorial above, you may have noticed that the create-aws-batch-env.bash script was p
    6 KB (1,036 words) - 17:51, 28 July 2022
  • How to Create Cluster 7 (Ubuntu 20.04)
    # [https://netways.github.io/foreman-training/static/#1 Here's a tutorial on Foreman]
    7 KB (785 words) - 22:36, 26 October 2021
  • DOCK 3.7 2015/04/15 abl1 Tutorial
    ...il 17, 2015. This tutorial is now superseded by[[DOCK 3.7 2018/06/05 abl1 Tutorial]]. See the following tutorial for updated scripts:
    28 KB (4,315 words) - 21:05, 19 October 2023
  • Coloring and Subcluster Matching
    ...enerated by the automatic way, you should be able to change them based the tutorial in this section. The last column of each matching sphere is a number that y
    8 KB (878 words) - 20:37, 12 April 2022
  • Build ChEMBL for SEA
    Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts
    6 KB (922 words) - 21:19, 22 June 2023
  • Protein Target Preparation Updated
    ...hange the radius in the "vdw.siz" file and then run QNIFFT again - see the tutorial on Parameter Scanning: ...statics.phi" files into DX files for opening in Chimera. See the following tutorial for visualizing electrostatics grids:
    16 KB (2,467 words) - 18:59, 10 October 2019
  • How to dock in DOCK3.8
    ...e premade db2.tgz files, for example from the zinc22 3D archive, start the tutorial here. ...this example is a suggestion applicable only if you've been following the tutorial up to this point.
    16 KB (2,599 words) - 22:28, 1 December 2022
  • Minimize protein-ligand complex with AMBER
    This tutorial is for Shoichet Lab group members but we hope that it might be useful to th
    7 KB (1,147 words) - 01:34, 15 December 2018
  • Slurm Installation Guide
    The current version at the time of this tutorial is 22.05.5
    8 KB (1,109 words) - 20:27, 22 March 2024
  • How to do indexing, partition, and migration in Postgres 10
    This tutorial shows how to do data migration, partition, and indexing in Postgres 10.
    10 KB (1,395 words) - 22:16, 3 August 2018
  • Generating decoys (Reed's way)
    All scripts for this tutorial can be found in:
    14 KB (2,220 words) - 07:49, 23 September 2022
  • DOCKovalent 3.7
    The rest of the tutorial will assume DOCKBASE is set.
    10 KB (1,665 words) - 14:36, 29 July 2019
  • DOCK 3.7 2018/06/05 abl1 Tutorial
    This tutorial use the 3.7.2 beta version of dock release on April 17, 2015. This part of the tutorial is tailored for shoichet lab use. An outside user of dock might need to de
    27 KB (4,088 words) - 21:04, 19 October 2023
  • GPCR modeling tips and tricks
    ...give them a quick look before committing to a larger ensemble. There is a tutorial [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html here].
    12 KB (1,840 words) - 01:13, 1 June 2017
  • Tutorial on running Molecular Dynamics for GIST grid generation
    Tutorial written by Trent Balius (Jan. 9, 2017). To use this tutorial you will need the following:
    26 KB (4,023 words) - 00:21, 5 March 2019
  • Tutorial on running Molecular Dynamics for GIST grid generation with scripts
    Tutorial written by Trent Balius (Jan. 9, 2017). To use this tutorial you will need the following:
    49 KB (7,168 words) - 00:18, 9 November 2017
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