User contributions for Frodo
Jump to navigation
Jump to search
14 February 2014
- 03:1403:14, 14 February 2014 diff hist +65 Get ZINC under program control No edit summary
- 03:0703:07, 14 February 2014 diff hist +42 Choosing a subset No edit summary current
- 03:0603:06, 14 February 2014 diff hist +104 Chemoinformatics Waiver Wire No edit summary
- 03:0503:05, 14 February 2014 diff hist +52 Chemdraw figure preparation No edit summary current
- 03:0403:04, 14 February 2014 diff hist +73 Chembl processing protocol No edit summary
- 03:0403:04, 14 February 2014 diff hist 0 Checkout dockenv No edit summary
- 03:0303:03, 14 February 2014 diff hist +79 Checkout dockenv No edit summary
- 03:0203:02, 14 February 2014 diff hist −51 ChEMBL API No edit summary
- 02:5902:59, 14 February 2014 diff hist +55 Cassidy clustering No edit summary
- 02:5802:58, 14 February 2014 diff hist +81 Calculate DOCK6 RMSD No edit summary
- 02:5702:57, 14 February 2014 diff hist +98 CSD No edit summary
- 02:5502:55, 14 February 2014 diff hist +76 Basic Tutorial No edit summary
- 02:5502:55, 14 February 2014 diff hist +53 SEA No edit summary
- 02:5402:54, 14 February 2014 diff hist +103 BKS lab Structure preparation No edit summary
- 02:5202:52, 14 February 2014 diff hist +45 Cluster 4 No edit summary
- 02:2202:22, 14 February 2014 diff hist −20 Category:DOCK 3.7 Blanked the page
- 02:1602:16, 14 February 2014 diff hist +20 N Category:DOCK 3.7 Created page with "{{catmain|DOCK 3.7}}"
13 February 2014
- 21:5121:51, 13 February 2014 diff hist −82 DOCK 3.6 No edit summary
- 21:4221:42, 13 February 2014 diff hist +31 DOCK 3.7 No edit summary
- 21:4121:41, 13 February 2014 diff hist +3,353 N Analyzing DOCK Results Created page with "Analyzing DOCK results The dock37tools in $d37 contain various analysis programs. Once your jobs are done, you can run: $d37/extract_all.py If your ran a prospective run, it..."
- 21:4021:40, 13 February 2014 diff hist +1,567 N Running DOCK 3.7 Created page with "Setting up an alias for the dock37tools directory in $DOCK_BASE/src/dock37tools/ is highly recommended, though you don't need it if you don't want it. Assume you have it set a..." current
- 21:3921:39, 13 February 2014 diff hist +4 DOCK 3.7 No edit summary
- 21:3821:38, 13 February 2014 diff hist +555 N ZINC Subset DB2 file locations Created page with "On the UCSF cluster: /raida/db/rgc/frags-now-marvin Fragments available now /raida/db/rgc/frags-all-marvin All fragments available now or on-demand quickly /raida/db/rgc/lead..."
- 21:3721:37, 13 February 2014 diff hist +3,536 N Flexible Docking Created page with """"Flexible Docking""" For citations and example use, please see Citations for DOCK3.7, Fischer, Coleman et al. Input for flexible docking requires a single PDB file with al..." current
- 21:3521:35, 13 February 2014 diff hist +672 N Adding Static Waters to the Protein Structure Created page with "If you have ordered waters in your structure, DOCK3.7 can use them, but you have to add hydrogens 'manually' using some visualization program and your intuition. Once this is ..."
- 21:3421:34, 13 February 2014 diff hist +1,669 N Protein Target Preparation Created page with "Protein Target Preparation be-blasti is still the preferred method of downloading PDB files and splitting them into rec.pdb and xtal-lig.pdb files. Run it with be_blasti.csh ..."
- 21:3121:31, 13 February 2014 diff hist +181 N Mol2db2 Created page with "mol2db2 is a program that takes multi-conformation mol2 files and compiles them into the db2 format for docking. {{Template:CC-BY-SA-30}} {{Template:Coleman}} [[Category:DOCK..."
- 21:3021:30, 13 February 2014 diff hist +2 DOCK 3.7 No edit summary
- 21:3021:30, 13 February 2014 diff hist +35 DOCK 3.7 No edit summary
- 21:2921:29, 13 February 2014 diff hist 0 Ligand preparation No edit summary
- 21:2821:28, 13 February 2014 diff hist +1,096 N Ligand preparation Created page with "Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SM..."
- 21:2721:27, 13 February 2014 diff hist +6,248 N Mol2db2 format Created page with "<pre> Mol2db2 Format 2 File Format T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."
- 21:2321:23, 13 February 2014 diff hist +4 DOCK 3.7 No edit summary
- 21:2221:22, 13 February 2014 diff hist +47 Analyzing DOCK 3.7 Results No edit summary current
- 21:2121:21, 13 February 2014 diff hist +4,710 N INDOCK 3.7 Created page with "<pre> DOCK 3.7 parameter ##################################################### # NOTE: split_database_index is reserved to specify a list of files ligand_atom_file ..."
- 21:1921:19, 13 February 2014 diff hist −2 DOCK 3.7 No edit summary
- 21:1821:18, 13 February 2014 diff hist +1 DOCK 3.7 No edit summary
- 21:1821:18, 13 February 2014 diff hist −25 DOCK 3.7 No edit summary
- 21:1721:17, 13 February 2014 diff hist +306 DOCK 3.7 No edit summary
- 21:1721:17, 13 February 2014 diff hist +175 N Template:Coleman Created page with "This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at [https://sites.google.com/site/dock37wiki/ https://sites.google.com/site/dock37wiki/]."
- 21:1621:16, 13 February 2014 diff hist −281 Template:CC-BY-SA-30 No edit summary
- 21:1021:10, 13 February 2014 diff hist +561 N Template:CC-BY-SA-30 Created page with "[Image:http://i.creativecommons.org/l/by-sa/3.0/88x31.png] This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of thi..."
- 21:0021:00, 13 February 2014 diff hist +3,440 N Analyzing DOCK 3.7 Results Created page with "Analyzing DOCK 3.7 results The dock37tools in $d37 contain various analysis programs. Once your jobs are done, you can run: $d37/extract_all.py If you ran a prospective run,..."
12 February 2014
- 20:0420:04, 12 February 2014 diff hist +69 N Hypervisor Created page with "ssh into the hypervisor (apes, rocky, pulp) sudo virsh list --all"
30 January 2014
- 17:1717:17, 30 January 2014 diff hist +166 N Disk full Created page with "if the disk is full, here is how you find out who the major culprits are (example here is /raid1) sudo /usr/sbin/repquota /raid1 | sort -nk3 [{Category:Internal]]"
29 January 2014
- 20:4520:45, 29 January 2014 diff hist +862 N Get ZINC under program control Created page with "More things to not forget <pre> teague:~$ wget -q --post-file smiles-to-lookup.smi "http://zinc.uoft.bkslab.org:8080/inchi -O- ZINC01586379 ZINC00000053 ZINC15202372 teague:..."
- 20:4320:43, 29 January 2014 diff hist +825 N Ring SQL query Created page with "From his bestseller, 101 things to not forget <pre> This just came out of some debugging. Thought you may be interested. It will return the number of occurrences of a particu..."
- 20:4020:40, 29 January 2014 diff hist +1,700 N Cassidy clustering Created page with "These are notes to myself from Teague/Cassidy for the new cluster. [[Category::Internal]] I've written some code to generate Daylight-like fingerprints (Base-64) from the ..."
27 January 2014
- 19:3319:33, 27 January 2014 diff hist +491 Github No edit summary
- 19:3019:30, 27 January 2014 diff hist +240 Nm User talk:Sedigheh Welcome! current
- 19:3019:30, 27 January 2014 diff hist +16 Nm User:Sedigheh Creating user page for new user. current
- 19:2919:29, 27 January 2014 diff hist +240 Nm User talk:Eric Walters Welcome! current
- 19:2919:29, 27 January 2014 diff hist +68 Nm User:Eric Walters Creating user page for new user. current
22 January 2014
- 18:1118:11, 22 January 2014 diff hist +1,464 N Adding memory to a virtual machine Created page with "Use "virsh", either locally: root@rocky$ virsh (COMMANDS HERE) or remotely: teague@spinaltap$ virsh --connect qemu:///rocky.cluster.uoft.bkslab.org/system (COMMANDS HERE) W..."
15 January 2014
- 19:4319:43, 15 January 2014 diff hist +797 N Zinc exact lookup by http Created page with "New ZINC lookup features wget -q --post-file smiles-to-lookup.smi "http://zinc.uoft.bkslab.org:8080/inchi -O- ZINC01586379 ZINC00000053 ZINC15202372 wget -q --post-file..."
10 January 2014
- 15:3715:37, 10 January 2014 diff hist −4 Category:Internal No edit summary
- 15:3715:37, 10 January 2014 diff hist +106 Category:Internal No edit summary
- 15:3315:33, 10 January 2014 diff hist −8 Lab Security Policy No edit summary
- 15:3215:32, 10 January 2014 diff hist −7 Lab Security Policy No edit summary
- 15:3115:31, 10 January 2014 diff hist +4 Lab Security Policy No edit summary
- 15:3115:31, 10 January 2014 diff hist +19 Lab Security Policy No edit summary
- 15:2915:29, 10 January 2014 diff hist +442 Lab Security Policy No edit summary
- 15:2315:23, 10 January 2014 diff hist −21 Lab Security Policy No edit summary
- 15:1915:19, 10 January 2014 diff hist +8 Lab Security Policy No edit summary
9 January 2014
- 21:1821:18, 9 January 2014 diff hist −42 SSH public key authentication Redirected page to How to generate ssh keys securely current
9 December 2013
- 21:1221:12, 9 December 2013 diff hist +240 Nm User talk:Shuiqing li Welcome! current
- 21:1221:12, 9 December 2013 diff hist +30 Nm User:Shuiqing li Creating user page for new user. current
12 November 2013
- 19:4219:42, 12 November 2013 diff hist +1,009 N Metabolites databases Created page with "There are two three kinds of metabolite docking databases at docking.org, and from each type, there are multiple actual databases. *NB this work is still in progress* = Gr..."
11 November 2013
- 20:3520:35, 11 November 2013 diff hist +3 Cluster 1 No edit summary
- 20:0820:08, 11 November 2013 diff hist +66 SVN No edit summary
- 20:0720:07, 11 November 2013 diff hist +121 N Github Created page with "This page describes how to use github, which is our version control system. Category:Internal Category:Sysadmin"
6 November 2013
- 17:3117:31, 6 November 2013 diff hist +29 Loading ZINC12 →2. Parse SDF into ISM, harvesting data from SD tags into synonyms table
- 17:3017:30, 6 November 2013 diff hist −29 Loading ZINC12 →4. Desalt, filter out neverwants, stereochemical expansion, remove N stereochem, take 4 max
- 17:2917:29, 6 November 2013 diff hist +28 Loading ZINC12 →4. Desalt, filter out neverwants, stereochemical expansion, remove N stereochem, take 4 max
- 17:2817:28, 6 November 2013 diff hist +58 Loading ZINC12 →2. Parse SDF into ISM, harvesting data from SD tags into synonyms table
- 16:3416:34, 6 November 2013 diff hist +828 Loading ZINC12 No edit summary
- 15:5015:50, 6 November 2013 diff hist +508 Loading ZINC12 No edit summary
4 November 2013
- 15:2615:26, 4 November 2013 diff hist +7 Category:Sysadmin No edit summary
- 15:2515:25, 4 November 2013 diff hist +379 N Category:Public Created page with "The public tag is the default and thus not necessary. Any page that is neither Internal nor Sysadmin is automatically considered Public. Roughly, pages on this site are cat..."
- 15:2415:24, 4 November 2013 diff hist +234 Category:Sysadmin No edit summary
- 15:2415:24, 4 November 2013 diff hist +367 Category:Internal No edit summary
- 14:5014:50, 4 November 2013 diff hist +161 N Category:Sysadmin Created page with "These are pages for docking.org sysadmins. This is a starting point and central node for anyone who wants to install, run and manage a docking.org site locally."
- 13:2413:24, 4 November 2013 diff hist +3,468 N Updating Rdkit Created page with " = Notes = Each version is now installed in $PYTHON_ROOT/local/rdkit-VERSION. The current version is a symlink now named $PYTHON_ROOT/local/rdkit. It's worth noting how this..."
2 November 2013
- 00:2500:25, 2 November 2013 diff hist +754 N Sysadmin guide to docking.org Created page with "This is what you need to know to be a sysadmin at docking.org or a docking.org clone site Worldwide ZINC. It will probably more of a checklist than a how to guide for some..."
- 00:1900:19, 2 November 2013 diff hist +33 Worldwide ZINC →Sites
- 00:1900:19, 2 November 2013 diff hist +832 N Worldwide ZINC Created page with "We have this crazy idea to replicate the lab in different sites around the world. We want to join these sites loosely together to that resources can be pooled, and improvement..."
- 00:1100:11, 2 November 2013 diff hist −50 DISI:Current events No edit summary
1 November 2013
- 23:4723:47, 1 November 2013 diff hist +763 N ZINC api Created page with "Here we explain how to access ZINC via an application programming interface (api) Please note that this is for zinc13 and beyond that is based on rdkit and psql. Previously,..."
31 October 2013
- 20:2220:22, 31 October 2013 diff hist +603 N How to spin up a new virtual machine Created page with "This is the step by step guide on how to create a new vm on a hypervisor, and how to configure it, log in , and, optionally, configure sge and nfs. It is designed to be used..."
- 20:1420:14, 31 October 2013 diff hist +1,569 N Docking.org install Created page with "This page describes how to set up a new docking.org site, part of the worldwide ZINC network. = Approaches = * 1. You can set up each machine separately, download each packa..."
- 20:0320:03, 31 October 2013 diff hist +21 Install DOCK 6 No edit summary
- 20:0320:03, 31 October 2013 diff hist +66 Workstation Install No edit summary
- 20:0220:02, 31 October 2013 diff hist +21 Install SEA No edit summary
- 20:0120:01, 31 October 2013 diff hist +59 Install DOCK 3 No edit summary
22 August 2013
- 18:1518:15, 22 August 2013 diff hist 0 Tool1 No edit summary
- 18:1518:15, 22 August 2013 diff hist +600 N Tool1 Created page with "= Tool2 aka SEAvis = = Question = What compounds contribute most to the SEA score between any two targets? = Approach = We have a tool (contact John for details). * Sp..."
- 18:1118:11, 22 August 2013 diff hist +1,932 N Tool2 Created page with " = Question = What is the most similar compound from any one catalog to my molecule? This could be any single catalog in ZINC. Currently you must specify the short name of t..."
21 August 2013
14 August 2013
- 21:5821:58, 14 August 2013 diff hist +239 Nm User talk:Aniello Palma Welcome! current
- 21:5821:58, 14 August 2013 diff hist +196 Nm User:Aniello Palma Creating user page for new user. current