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Combined display of all available logs of DISI. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 21:42, 20 September 2023 Omailhot talk contribs created page Olivier's way of computing novelty (Created page with "This is my lazy way of doing novelty calculations. '''Step 0: source my environment''' All I'm developing is part of a single Python package called bksltk (BKS-lab Toolkit). So just source my Python environment on gimel2 (or other gimelX which has Python3) and you'll have access to everything: source /nfs/home/omailhot/pyenv_source.sh Eventually the package will be better documented (and probably integrated into pydock). '''Step 1: get all knowns from ChEMBL''' H...")
- 20:57, 20 September 2023 Khtang talk contribs created page Chemistry commons Notes (Created page with "== Database Management == Source chemistry commons source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons === Import data from Spreadsheet === ** This will be deprecated once we switched to use postgres bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx] === Export Chemistry Commons DB === Run this script to create a snapshot of the database and JSON files for Enum...")
- 21:08, 12 September 2023 Jgutierrez6 talk contribs created page Rack Power (PDUs) (Created page with "== Introduction == This page will detail what PDUs are in which rack and how much Amperage they can hold. It will also detail how much max Amperage each machine can draw from the PDUs. == Power Table ==")
- 20:16, 29 August 2023 Ianscottknight talk contribs moved page TLDR:dude-z to TLDR:decoygen (Naming the decoy generation pipeline `dude-z` doesn't really make sense given that DUDE-Z is a dataset. I am guessing that the original logic behind this was that the pipeline was used to help create DUDE-Z. Still, the data types `pipeline` and `dataset` are distinct, therefore justifying this name change.)
- 01:44, 24 August 2023 Ianscottknight talk contribs created page File:Pydock3 logo.png
- 01:44, 24 August 2023 Ianscottknight talk contribs uploaded File:Pydock3 logo.png
- 18:51, 10 August 2023 Mtsukanov talk contribs created page CLI Enumeration (Created page with "== Coding the Reactions == Step 1. Pick out the reactions that you want to enumerate. This can be done either through already-made reactions that are in commons.docking.org or you can use those reaction SMARTS and inclusion/exclusion SMARTS as examples/guidelines to make your own reaction/s. We recommend using the daylight SMARTS as a resource if you plan on doing this: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. Once you have your reaction we recomme...")
- 00:13, 14 June 2023 Btingle talk contribs created page All About DB2 Files (Created page with "== The brass tacks == DB2 files encode & compress 3D molecule rotomers, sometimes referred to as conformations. DB2 files do not store the dihedral angles of rotomers, but instead the per-atom coordinates resulting from those angles Atoms of different rotomers whose coordinates overlap are merged together in db2 files (how this is done will be detailed more later), thus allowing DOCK to avoid double-calculating per-atom energies == The nitty gritty == DB2 is a text fo...")
- 22:21, 31 May 2023 Btingle talk contribs created page Installing The 3D Pipeline ZINC22 (Created page with "Installation of the 3D pipeline is somewhat tricky- the environment is very particular about which versions of which software should be used. It is thus easiest to copy the exact software packages we use from our servers- this should work provided they are installed in a 64-bit linux architecture, though depending on the distribution certain shared libraries may be missing. == Setting up the installation root == First find a suitable directory which will serve as the r...")
- 21:20, 23 May 2023 Mtsukanov talk contribs created page Particle Shape Calculator for CCDC/Mercury (Created page with "This tutorial will introduce you to the morphology calculation features included with Mercury under the CSD-Particle toolset, namely BFDH Morphology and VisualHabit. BFDH crystal morphology is an approximation based on crystallographic geometrical considerations. For a given structure, the BFDH algorithm will predict the habit or shape of a crystal using the corresponding unit cell and symmetry operator information. The VisualHabit tool calculates a morphology for your m...")
- 23:01, 1 May 2023 Iamkaant talk contribs created page File:Combined metrics plot from a GA run.png
- 23:01, 1 May 2023 Iamkaant talk contribs uploaded File:Combined metrics plot from a GA run.png
- 06:58, 30 April 2023 Iamkaant talk contribs created page Global Matching Sphere Optimization (Created page with "== Goal == To optimize your matching sphere (MS) setups getting more enrichment with fewer spheres. == Description == The program performs optimization of matching spheres using genetic algorithm. It selects spheres from two sets: * heavy atoms of xtal-lig * spheres prepared by SPHGEN program At each generation, N matching sphere sets are created, containing a maximum of M spheres each. Then retrospective docking is done for each set, and sets are ranked by the enrichme...")
- 21:57, 25 April 2023 Frodo talk contribs created page How to release DOCK (asdf)
- 19:02, 19 April 2023 Saadamin2006 talk contribs created page GPU DOCK (Created page with "# GPU DOCK Wiki GPU DOCK is a fork of DOCK 3.8 that utilizies GPU acceleration via CUDA. Currently (as of April 2023) GPU DOCK uses the GPU for parallel scoring and only supports Van der Waals, electrostatics, and solvation scores. # Running and Building GPU DOCK The main files for GPU DOCK are in the `DOCK/ucsfdock/docking/DOCK/src` directory of DOCK. There are a few important scripts here: * `clean.sh` that clears object files from previous builds * `compile.sh` wh...")
- 15:25, 19 April 2023 Frodo talk contribs created page User talk:Saadamin2006 (Welcome!)
- 15:25, 19 April 2023 Frodo talk contribs created page User:Saadamin2006 (Creating user page for new user.)
- 15:25, 19 April 2023 User account Saadamin2006 talk contribs was created by Frodo talk contribs and password was sent by email (welcome)
- 22:24, 12 April 2023 Frodo talk contribs created page Search (asdf)
- 17:40, 12 April 2023 Frodo talk contribs created page Standup tuesday (asdf)
- 18:16, 31 March 2023 Frodo talk contribs created page Properties (asdf)
- 16:10, 31 March 2023 Frodo talk contribs created page Installing DOCK6 on Apple Silicon M2 (asdf)
- 17:49, 23 March 2023 Frodo talk contribs created page OCI:More work (asdf)
- 19:49, 22 March 2023 Frodo talk contribs created page OCI:Create account (asdf)
- 18:35, 22 March 2023 Frodo talk contribs created page OCI:Set up account (asdf)
- 18:50, 21 March 2023 Mtsukanov talk contribs created page AB3 Developer Notes (Created page with "'''UNDER DEVELOPMENT''' The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first...")
- 22:24, 20 March 2023 Frodo talk contribs created page Covalent library preparation 2023 (qasdf)
- 20:21, 15 March 2023 Frodo talk contribs created page TLDR:enumeration (asdf)
- 19:42, 15 March 2023 Frodo talk contribs created page TLDR:bbfilter (asdf)
- 22:32, 13 March 2023 Khtang talk contribs created page LUNA (Created page with "'''LUNA''' is drug discovery Python toolkit developed by Keiser Lab at UCSF Github repo https://github.com/keiserlab/LUNA == Install Instruction == If you have trouble following LUNA's conda environment setup instruction, try this conda create -n luna-env -c schrodinger pymol -y conda activate luna-env conda install -c conda-forge rdkit seaborn openbabel pip xopen colorlog networkx -y pip install mmh3==2.5.1 pip install biopython==1.72 BKS Cluster has LUNA conda...")
- 20:29, 2 March 2023 Btingle talk contribs created page Repackaging DB2 DOCK38 (Created page with "The following is a script for repackaging 3D pipeline results. First, here is the script: <nowiki> #!/bin/bash # make_tarballs.bash # required parameter RESULT_DIRECTORY=$1 # optional parameters WORKING_DIRECTORY=${WORKING_DIRECTORY-/tmp/$(whoami)} PACKAGES_PER_PACKAGE=${PACKAGES_PER_PACKAGE-100} PACKAGE_TYPE=${PACKAGE_TYPE-db2.gz} PACKAGE_TYPE_SHORT=$(echo $PACKAGE_TYPE | cut -d'.' -f1) echo WORKING_DIRECTORY=$WORKING_DIRECTORY mkdir -p $WORKING_DIRECTORY && cd $WO...")
- 21:56, 22 February 2023 Jgutierrez6 talk contribs created page How to use Arthor Command Line (Created page with "== Introduction == Here is an introduction on how to use the Arthor commands in the command line for substructure searching. == Important Information == *Arthor Databases are backed up in '''/nfs/exj/arthor_db_backup/'''. *Arthor version will differ as time goes on but the command line should be fairly the same. == Simple use of Arthor Commands == # Export the Arthor bin path to use executables #: <source> export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-3.4.7/arthor...")
- 19:38, 21 February 2023 Jgutierrez6 talk contribs created page How to use Smallworld Java Command Line (Created page with "== How to use Smallworld Java Command Line == # Use bash as your shell #* <source>bash //just type in bash and enter</source> # Export these variables #* <source> export SWDIR=/mnt/nfs/db3/public_smallworld_5th_gen export sw='java -jar /nfs/db3/smallworld-5.5/sw.jar' </source> # Run the similarity command and it will display what it can do #* <source> $sw sim </source> # The path of the databases you can search from is here #* /mnt/nfs/db3/public_smallworld_5th_gen/maps/...")
- 21:52, 16 February 2023 Frodo talk contribs created page How to create actives and decoys for dockopt (asdf)
- 21:47, 16 February 2023 Frodo talk contribs created page Docking configuration (asdf)
- 19:31, 8 February 2023 Frodo talk contribs created page Caveat Emptor (asdf)
- 23:03, 20 January 2023 Omailhot talk contribs created page File:Mor zoom example.gif
- 23:03, 20 January 2023 Omailhot talk contribs uploaded File:Mor zoom example.gif
- 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor3.png
- 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor3.png
- 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor2.png
- 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor2.png
- 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor1.png
- 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor1.png
- 21:53, 20 January 2023 Omailhot talk contribs created page File:Chemspace vis example.gif
- 21:53, 20 January 2023 Omailhot talk contribs uploaded File:Chemspace vis example.gif
- 00:40, 20 January 2023 Omailhot talk contribs created page File:Chemspace vis example1.png
- 00:40, 20 January 2023 Omailhot talk contribs uploaded File:Chemspace vis example1.png
- 00:38, 20 January 2023 Jgutierrez6 talk contribs created page File:Sunflower.jpeg (Test Upload)
- 00:38, 20 January 2023 Jgutierrez6 talk contribs uploaded File:Sunflower.jpeg (Test Upload)
- 00:38, 20 January 2023 Omailhot talk contribs created page Interactive ligands visualizer (Created page with "I (Olivier) put together this interactive visualizer to make sure that I don't miss out some chemotypes when coming up with actives at the start of a retrospective campaign. Starting from a downloaded ChEMBL CSV file for a list of ligands, images of each molecule are generated with RDKit and a text file with filtered Smiles is generated. You then need to compute the ECFP fingerprints on Gimel from that file (see below), and then a generated script will show an interactiv...")
- 17:12, 13 January 2023 Frodo talk contribs created page User talk:H-arima (Welcome!)
- 17:12, 13 January 2023 Frodo talk contribs created page User:H-arima (Creating user page for new user.)
- 17:12, 13 January 2023 User account H-arima talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 20:40, 2 January 2023 Cbedart talk contribs created page CB Iridium (Created page with "== 0. Table of CB bespoke libraries == The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical libra...")
- 23:59, 15 December 2022 Jgutierrez6 talk contribs created page File:Globus personal.png
- 23:59, 15 December 2022 Jgutierrez6 talk contribs uploaded File:Globus personal.png
- 23:58, 15 December 2022 Jgutierrez6 talk contribs deleted page File:Collection.png (not needed anymore)
- 23:57, 15 December 2022 Jgutierrez6 talk contribs created page File:Globus share.png
- 23:57, 15 December 2022 Jgutierrez6 talk contribs uploaded File:Globus share.png
- 00:35, 15 December 2022 Frodo talk contribs created page User talk:Muhammad shofi (Welcome!)
- 00:35, 15 December 2022 Frodo talk contribs created page User:Muhammad shofi (Creating user page for new user.)
- 00:35, 15 December 2022 User account Muhammad shofi talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 00:35, 15 December 2022 Frodo talk contribs created page User talk:Fconsoli (Welcome!)
- 00:35, 15 December 2022 Frodo talk contribs created page User:Fconsoli (Creating user page for new user.)
- 00:35, 15 December 2022 User account Fconsoli talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 16:20, 13 December 2022 Cbedart talk contribs created page CB DOCK 3.8 tutorial (Creation)
- 21:51, 1 December 2022 Jgutierrez6 talk contribs created page Smallworld and Arthor Databases (Created page with "== Introduction ==")
- 02:14, 1 December 2022 Btingle talk contribs created page SUBDOCK DOCK3.8 (Created page with "== how to use subdock == Subdock is a utility for running UCSF docking workloads across multiple platforms. There are four essential ingredients that go in to every docking...")
- 06:18, 4 November 2022 Khtang talk contribs created page Slurm Installation Guide (Created page with "This page will show you how to setup and configure a Slurm queueing system. Useful link: https://wiki.fysik.dtu.dk/Niflheim_system/Slurm_installation/ == Pre-installation ==...")
- 20:38, 19 October 2022 Btingle talk contribs created page File:Step1-docktut-again.png
- 20:38, 19 October 2022 Btingle talk contribs uploaded File:Step1-docktut-again.png
- 20:33, 19 October 2022 Btingle talk contribs created page File:Stepwhatever2.png
- 20:33, 19 October 2022 Btingle talk contribs uploaded File:Stepwhatever2.png
- 20:33, 19 October 2022 Btingle talk contribs created page File:Stepwhatever.png
- 20:33, 19 October 2022 Btingle talk contribs uploaded File:Stepwhatever.png
- 20:25, 19 October 2022 Btingle talk contribs created page File:Step6.png
- 20:25, 19 October 2022 Btingle talk contribs uploaded File:Step6.png
- 20:21, 19 October 2022 Btingle talk contribs created page File:Awsdock-Step3-flowchart.png
- 20:21, 19 October 2022 Btingle talk contribs uploaded File:Awsdock-Step3-flowchart.png
- 20:15, 19 October 2022 Btingle talk contribs created page File:Step3.png
- 20:15, 19 October 2022 Btingle talk contribs uploaded File:Step3.png
- 20:12, 19 October 2022 Btingle talk contribs created page File:Awsdock-imagetut-step1.png
- 20:12, 19 October 2022 Btingle talk contribs uploaded File:Awsdock-imagetut-step1.png
- 17:50, 28 September 2022 Frodo talk contribs created page ZINC22:Numbering (asdf)
- 23:23, 14 September 2022 Frodo talk contribs created page Programming DOCK 3.8 (asdf)
- 21:29, 14 September 2022 Frodo talk contribs created page AWS:Cleanup (asdf)
- 21:20, 14 September 2022 Frodo talk contribs created page Category:Tutorial (asd)
- 20:41, 14 September 2022 Frodo talk contribs moved page Docking Analysis On AWS to AWS:Merge and download results (clarity)
- 20:39, 14 September 2022 Frodo talk contribs moved page Docking Submission On AWS to AWS:Submit docking job (clarity)
- 20:38, 14 September 2022 Frodo talk contribs moved page AWS DOCK Environment Setup to AWS:Set up account (clarify)
- 20:36, 14 September 2022 Frodo talk contribs created page AWS:Upload files for docking (asdf)
- 22:25, 13 September 2022 Frodo talk contribs created page AWS:Track costs (asdf)
- 19:53, 12 September 2022 Frodo talk contribs created page DOCK 3.8:How to build a release (asdf)
- 19:46, 12 September 2022 Frodo talk contribs moved page How to install pydock3 to DOCK 3.8:How to install pydock3 (package convention)
- 19:45, 12 September 2022 Frodo talk contribs moved page Pydock3 to DOCK3.8:Pydock3 (package naming convention)
- 17:30, 6 September 2022 Frodo talk contribs created page User talk:Cbedart (Welcome!)
- 17:30, 6 September 2022 Frodo talk contribs created page User:Cbedart (Creating user page for new user.)
- 17:30, 6 September 2022 User account Cbedart talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 17:05, 2 September 2022 Frodo talk contribs deleted page DOCK on AWS (content was: "DOCK on AWS = First time set up = * 1. create an account https://docs.aws.amazon.com/batch/latest/userguide/spot_fleet_IAM_role.html#spot-fleet-roles-cli define these roles AmazonEC2SpotFleetRole, AWSServiceRoleForEC2Spot and AWSServiceRoleForEC2SpotFleet. * 2. create awsuser (optional!) * 3. create an S3 bucket "results2021" within create dockfiles, database.txt output1 * 4....", and the only contributor was "Frodo" (talk))
- 08:12, 2 September 2022 Ianscottknight talk contribs created page Dockopt (pydock3 script) (Created page with "''dockopt'' allows the generation of many different docking configurations which are then evaluated & analyzed in parallel using a specified job scheduler (e.g. Slurm). The n...")
- 08:10, 2 September 2022 Ianscottknight talk contribs created page Blastermaster (pydock3 script) (Created page with "''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand. == ''init'' == First you need to create the file structure for y...")
- 06:39, 2 September 2022 Ianscottknight talk contribs created page Pydock3 (Created page with "''pydock3'' is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular...")
- 06:39, 2 September 2022 Ianscottknight talk contribs created page How to install pydock3 (Created page with "pydock3 is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular...")
- 22:48, 1 September 2022 Jgutierrez6 talk contribs created page How to Set Up Webalizer (Created page with "== Introduction == Webalizer creates and keeps track of user traffic on a website. == Instruction ==")
- 22:39, 1 September 2022 Khtang talk contribs created page User talk:Omailhot (Welcome!)
- 22:39, 1 September 2022 Khtang talk contribs created page User:Omailhot (Creating user page for new user.)
- 22:39, 1 September 2022 User account Omailhot talk contribs was created by Khtang talk contribs and password was sent by email
- 19:39, 1 September 2022 Jgutierrez6 talk contribs created page How to Relay Emails to Gmail (Created page with "== Introduction == This tutorial applies to RHEL 8 based operating systems (CentOS, Rocky Linux) Two machines that send emails are: *vav.combpio.ucsf.edu *bksmailman.compbio....")
- 19:01, 1 September 2022 Frodo talk contribs created page DOCK38:Job configuration (asdf)
- 18:09, 30 August 2022 Frodo talk contribs created page Copy protect in google docs (asdf)
- 19:25, 29 August 2022 Frodo talk contribs created page CC:Arthor (asdf)
- 19:24, 29 August 2022 Frodo talk contribs created page CC:Smallworld (asdf)
- 19:09, 29 August 2022 Frodo talk contribs deleted page Catagory:CC (Author request: content was: "Chemistry Commons articles.", and the only contributor was "Frodo" (talk))
- 19:03, 29 August 2022 Frodo talk contribs created page Catagory:CC (asdf)
- 19:03, 29 August 2022 Frodo talk contribs created page CC:Library preparation (asdf)
- 05:13, 29 August 2022 Mtsukanov talk contribs created page Bioisostere Tool (Created page with "BAT or Bioisostere Analoging Tool is a tool designed by the Irwin Lab for the purpose of analoging molecules. The tool creates analogs through interchanging the substructures...")
- 23:31, 27 August 2022 Mtsukanov talk contribs created page ABBB (Created page with "ABBB or Analog By Building Block is a tool designed by the Irwin Lab for the purpose of analogizing molecules. The molecules that are given to the tool are first retrosynthesi...")
- 16:19, 19 August 2022 Frodo talk contribs created page User talk:Wyujin (Welcome!)
- 16:19, 19 August 2022 Frodo talk contribs created page User:Wyujin (Creating user page for new user.)
- 16:19, 19 August 2022 User account Wyujin talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 16:17, 19 August 2022 Frodo talk contribs created page User talk:Sooikchae (Welcome!)
- 16:17, 19 August 2022 Frodo talk contribs created page User:Sooikchae (Creating user page for new user.)
- 16:17, 19 August 2022 User account Sooikchae talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 16:17, 19 August 2022 Frodo talk contribs created page User talk:Jjgutierrez6 (Welcome!)
- 16:17, 19 August 2022 Frodo talk contribs created page User:Jjgutierrez6 (Creating user page for new user.)
- 16:17, 19 August 2022 User account Jjgutierrez6 talk contribs was created by Frodo talk contribs and password was sent by email (welcome)
- 00:16, 18 August 2022 Frodo talk contribs created page TLDR:Library Enumeration (asdf)
- 00:15, 18 August 2022 Frodo talk contribs created page AB3 (asdf)
- 20:22, 10 August 2022 Jgutierrez6 talk contribs created page User talk:Test-Test (Welcome!)
- 20:22, 10 August 2022 Jgutierrez6 talk contribs created page User:Test-Test (Creating user page for new user.)
- 20:22, 10 August 2022 User account Test-Test talk contribs was created by Jgutierrez6 talk contribs and password was sent by email (to test)
- 22:44, 9 August 2022 Jgutierrez6 talk contribs created page User talk:Test (Welcome!)
- 22:44, 9 August 2022 Jgutierrez6 talk contribs created page User:Test (Creating user page for new user.)
- 22:44, 9 August 2022 User account Test talk contribs was created by Jgutierrez6 talk contribs and password was sent by email
- 18:58, 9 August 2022 Frodo talk contribs created page AWS:Upload docking files to aws (asd)
- 18:50, 9 August 2022 Frodo talk contribs created page ZINC-22:Select chemical space for docking (asdf)
- 16:40, 9 August 2022 Frodo talk contribs created page Category:Cloud (Created page with "This is where we organize main organizing articles about using DOCK in the Cloud.")
- 16:40, 9 August 2022 Frodo talk contribs created page Category:OCI (asdf)
- 16:37, 9 August 2022 Frodo talk contribs created page Preparing dockfiles using TLDR (asdf)
- 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Swbatch to TLDR:swbatch without leaving a redirect
- 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Strain to TLDR:strain without leaving a redirect
- 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Newbuild3d to TLDR:newbuild3d without leaving a redirect
- 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Extrema to TLDR:extrema without leaving a redirect
- 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:DUDE-Z to TLDR:dude-z without leaving a redirect
- 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:Bootstrap2 to TLDR:bootstrap2
- 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:Bootstrap1 to TLDR:bootstrap1 without leaving a redirect
- 05:27, 9 August 2022 Khtang talk contribs moved page TLDR:Bioisostere to TLDR:bioisostere without leaving a redirect
- 05:26, 9 August 2022 Khtang talk contribs moved page TLDR:Arthorbatch to TLDR:arthorbatch without leaving a redirect
- 06:15, 8 August 2022 Khtang talk contribs created page TLDR:Swbatch (Created page with "== Purpose == Running multiple queries on SmallWorld. See https://sw.docking.org/search.html == Inputs == * molecules.ism == Outputs == TBD == Notes == TBD")
- 06:12, 8 August 2022 Khtang talk contribs created page TLDR:Newbuild3d (Created page with "== Purpose == Prepare a 3D library for docking with '''DOCK3.8''' pipeline in several formats used by popular docking programs: sdf, db2, mol2, pdbqt, solv == Inputs == * mol...")
- 05:37, 8 August 2022 Khtang talk contribs created page TLDR:Extrema (Created page with "== Purpose == Generate an equivalent number of charged (-2, -1, 0, +1, +2) molecules in the molecular weight and cLogP property space of your input SMILES molecules. These cha...")
- 05:32, 8 August 2022 Khtang talk contribs created page TLDR:Bootstrap2 (Created page with "== Purpose == Get 95% confidence interval from bootstrapping. == Inputs == * decoys.name * ligands.name * ranked_list_1 * ranked_list_2 == Outputs == TBD == Notes == TBD")
- 05:30, 8 August 2022 Khtang talk contribs created page TLDR:Bootstrap1 (Created page with "== Purpose == Compare performance of 2 docking methods with p value == Inputs == * decoys.name * ligands.name * ranked_list_1 * ranked_list_2 == Outputs == TBD == Notes == TBD")
- 05:20, 8 August 2022 Khtang talk contribs created page TLDR:Strain (Created page with "== Purpose == This strain filter software is a fast and reliable approach to calculate the strain energy of millions of small molecules. == Inputs == * mol2 file contains mole...")
- 04:55, 8 August 2022 Khtang talk contribs created page TLDR:DUDE-Z (Created page with "== Purpose == Assemble decoys for docking using the DUDEZ approach. See https://dudez.docking.org for sample data == Inputs == * Ligands provided in smiles format (actives.sm...")
- 04:45, 8 August 2022 Khtang talk contribs created page TLDR:Bioisostere (Created page with "== Purpose == To find analogs of your active compounds that you can use to explore SAR by catalogs around your hits. == Inputs == * a starting molecule in txt file (one at a...")
- 19:56, 7 August 2022 Frodo talk contribs created page User talk:HusseinAli (Welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User:HusseinAli (Creating user page for new user.)
- 19:56, 7 August 2022 User account HusseinAli talk contribs was created by Frodo talk contribs and password was sent by email (Welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User talk:Cangfeng (Welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User:Cangfeng (Creating user page for new user.)
- 19:56, 7 August 2022 User account Cangfeng talk contribs was created by Frodo talk contribs and password was sent by email (welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User talk:E.zeqiraj (Welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User:E.zeqiraj (Creating user page for new user.)
- 19:56, 7 August 2022 User account E.zeqiraj talk contribs was created by Frodo talk contribs and password was sent by email (welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User talk:S1giard (Welcome!)
- 19:56, 7 August 2022 Frodo talk contribs created page User:S1giard (Creating user page for new user.)
- 19:56, 7 August 2022 User account S1giard talk contribs was created by Frodo talk contribs and password was sent by email (welcome!)
- 19:50, 7 August 2022 Frodo talk contribs created page ZINC22:Directory structure (asdf)
- 19:35, 7 August 2022 Frodo talk contribs moved page UCSF License to UCSF ZINC License (fix the name)
- 19:20, 7 August 2022 Frodo talk contribs created page UCSF License (asfd)
- 20:20, 5 August 2022 Jocastanon talk contribs created page Cartblanche22 Build Instructions (Created page with "== Local environment == * Clone repo Git clone https://gitlab.docking.org/chinzo/molecule-shopping-cart Cd molecule-shopping-cart * Create conda environment with python 3...")
- 17:53, 5 August 2022 Khtang talk contribs created page User talk:Jocastanon (Welcome!)
- 17:53, 5 August 2022 Khtang talk contribs created page User:Jocastanon (Creating user page for new user.)
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- 21:54, 4 August 2022 Khtang talk contribs created page Dimorphite-DL (Created page with "'''Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by [https://durrantlab.pitt.edu/ Durrant Lab] at University of Pittsburgh.''...")
- 20:48, 3 August 2022 Btingle talk contribs created page Using AWS Setup For Cloud Computation (Created page with "= Introduction to the AWS Setup platform = The concept of "the cloud" as a platform for computation is somewhat mystified. Scientists talk about running their calculations "i...")
- 20:44, 3 August 2022 Iamkaant talk contribs created page Synthesia (Created page with "<blockquote>Synthesia is a command-line tool that uses an entire retrosynthetic route as a guide pathway to generate optimized structural analogues of a lead compound without...")
- 20:09, 28 July 2022 Frodo talk contribs created page Category:TLDR (asdf)
- 18:55, 28 July 2022 Frodo talk contribs created page TLDR:Arthorbatch (asdf)
- 07:52, 28 July 2022 Ianscottknight talk contribs created page Ucsfdock (Created page with "`ucsfdock` is a Python package wrapping the DOCK program that provides tools to help standardize and automate the computational methods surrounding molecular docking....")
- 06:06, 27 July 2022 Btingle talk contribs created page AWS DOCK Environment Setup Advanced Usage (Created page with "= Advanced Usage/Configuration Usage = If you followed the tutorial above, you may have noticed that the create-aws-batch-env.bash script was provided a file, awsdock.config,...")
- 16:57, 26 July 2022 Btingle talk contribs created page File:Spotlimits.png
- 16:57, 26 July 2022 Btingle talk contribs uploaded File:Spotlimits.png
- 22:52, 25 July 2022 Khtang talk contribs created page File:Target vs target.png
- 22:52, 25 July 2022 Khtang talk contribs uploaded File:Target vs target.png
- 22:51, 25 July 2022 Khtang talk contribs created page File:Compound vs target.png
- 22:51, 25 July 2022 Khtang talk contribs uploaded File:Compound vs target.png
- 22:51, 25 July 2022 Khtang talk contribs created page File:Compound vs library.png
- 22:51, 25 July 2022 Khtang talk contribs uploaded File:Compound vs library.png
- 22:14, 25 July 2022 Ianscottknight talk contribs created page Dockmaster (Created page with "Dockmaster enables the efficient search for the optimal DOCK parameters of a given target receptor as evaluated by the amount of enrichment witnessed in retrospective docking....")
- 22:04, 25 July 2022 Ianscottknight talk contribs created page INDOCK (Created page with "The INDOCK file is the main parameters file of the DOCK program. It is a text file where each line specifies a parameter or the path to another parameter file. = Ver...")
- 16:59, 25 July 2022 Btingle talk contribs created page DOCK memory and CPU benchmark (Created page with "Excerpt from email between Ben Tingle and Jiankun Lyu: <nowiki> JK- I have some more info on how threads/cpus work. It seems that utilizing threads does give more power, but...")
- 03:30, 22 June 2022 Btingle talk contribs created page Category:AWS DOCK (Created page with "Protocols for running DOCK software on AWS. Specifically DOCK 3.8 (and others in the DOCK3 family) Despite these protocols being tailored for the DOCK3 family of software, th...")
- 00:15, 22 June 2022 Btingle talk contribs created page File:S3pricing.png
- 00:15, 22 June 2022 Btingle talk contribs uploaded File:S3pricing.png
- 23:53, 21 June 2022 Btingle talk contribs created page Docking Submission On AWS (Created page with "=== Prerequisites === * You've followed the tutorial for setting up the environment: AWS DOCK Environment Setup * Following from the previous requirement, you have the a...")
- 23:07, 21 June 2022 Btingle talk contribs created page File:Aws docking env.png
- 23:07, 21 June 2022 Btingle talk contribs uploaded File:Aws docking env.png
- 00:19, 18 June 2022 Btingle talk contribs created page File:Terminateinstance.png
- 00:19, 18 June 2022 Btingle talk contribs uploaded File:Terminateinstance.png
- 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched3.png
- 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched3.png
- 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched2.png
- 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched2.png
- 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched1.png
- 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched1.png
- 00:15, 18 June 2022 Btingle talk contribs created page File:Configstorage.png
- 00:15, 18 June 2022 Btingle talk contribs uploaded File:Configstorage.png
- 00:15, 18 June 2022 Btingle talk contribs created page File:Keypair.png
- 00:15, 18 June 2022 Btingle talk contribs uploaded File:Keypair.png
- 00:13, 18 June 2022 Btingle talk contribs created page File:Instancetype.png
- 00:13, 18 June 2022 Btingle talk contribs uploaded File:Instancetype.png
- 00:13, 18 June 2022 Btingle talk contribs created page File:Launchinstances.png
- 00:13, 18 June 2022 Btingle talk contribs uploaded File:Launchinstances.png
- 23:42, 17 June 2022 Btingle talk contribs created page Docking Analysis On AWS (Created page with "=== Prerequisites === github personal access token & DOCK repository access rights (https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-...")
- 18:34, 17 June 2022 Frodo talk contribs created page User talk:Siswandono (Welcome!)
- 18:34, 17 June 2022 Frodo talk contribs created page User:Siswandono (Creating user page for new user.)
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- 18:14, 17 June 2022 Frodo talk contribs created page Curation of ZINC-22 3D (asdf)
- 23:16, 13 June 2022 Btingle talk contribs created page OCI Slurm Autoscaling (Created page with "* Create a compartment for your autoscaling resources <nowiki> SlurmAutoScaling</nowiki> * Create a dynamic group for autoscaling instances. Add the following as a matching...")
- 21:48, 8 June 2022 Btingle talk contribs created page Search zinc22.py (Created page with " <nowiki> usage: search_zinc22.py [-h] [--configuration-server-url CONFIGURATION_SERVER_URL] zinc_id_in results_out positional...")
- 21:14, 6 June 2022 Iamkaant talk contribs created page Conversion of .rxn files to reaction SMARTS (Created page with "DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041 They store reactions in .rxn format, which is documented in...")
- 17:21, 21 May 2022 Frodo talk contribs created page ABBBR (abc)
- 21:40, 19 May 2022 Btingle talk contribs created page Legacy IDs in ZINC22 (Created page with "ZINC22 is by far the largest chemical database this lab has built, and with it's fantastic size we have found fantastic new difficulties. When we receive chemical libraries f...")
- 17:29, 19 May 2022 Frodo talk contribs created page User talk:Mtsukanov (Welcome!)
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- 20:46, 11 May 2022 Jgutierrez6 talk contribs created page Self-Signed SSL Certificate / Certbot (Created page with "== Introduction == We self sign our SSL Certificates for our websites proxied at these machines: *files2 *vav *bksmailman == How to Self-Sign a Website ==")
- 18:14, 3 May 2022 Frodo talk contribs created page User talk:We prasetyo (Welcome!)
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- 22:45, 12 April 2022 Khtang talk contribs created page Chemspace API (Created page with "This is a quick guide on how to use Chemspace API to get pricing information. Link to Chem-space's API https://api.chem-space.com/docs/ == Email info@chem-space.com to obtain...")
- 21:52, 8 April 2022 Khtang talk contribs moved page Tools18 to TLDR
- 19:18, 7 April 2022 Frodo talk contribs created page Methods section (asdf)
- 19:18, 6 April 2022 Khtang talk contribs created page Mem2 (Created page with "There are 3 postgres instances running on mem2. == Some useful commands == \l \\ list all databases \dt \\ list all relations (or tables) \du \\ list all users \dn \\ lis...")
- 19:59, 30 March 2022 Frodo talk contribs created page User talk:OsTrade Chemical Co (Welcome!)
- 19:59, 30 March 2022 Frodo talk contribs created page User:OsTrade Chemical Co (Creating user page for new user.)
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- 19:57, 30 March 2022 Frodo talk contribs created page User talk:Gbigbi (Welcome!)
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- 19:57, 30 March 2022 Frodo talk contribs created page User talk:Z1109615733 (Welcome!)