User contributions for Oliv Eidam
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17 May 2013
8 May 2013
- 21:4821:48, 8 May 2013 diff hist +197 Dock Sampling No edit summary
- 21:3721:37, 8 May 2013 diff hist +2,012 Dock Sampling No edit summary
- 21:0021:00, 8 May 2013 diff hist +447 Dock Sampling →2. Calculate RMSD values for all orientations compared to the crystal structure pose
- 20:5720:57, 8 May 2013 diff hist −1 Dock Sampling →Bioactive conformation sampled?
- 19:3319:33, 8 May 2013 diff hist +7 Tools for protein and ligand analysis No edit summary
- 19:3319:33, 8 May 2013 diff hist −1 Tools for protein and ligand analysis No edit summary
- 19:3219:32, 8 May 2013 diff hist +25 Tools for protein and ligand analysis No edit summary
- 19:3119:31, 8 May 2013 diff hist −16 Tools for protein and ligand analysis No edit summary
- 19:3019:30, 8 May 2013 diff hist +283 Tools for protein and ligand analysis No edit summary
- 19:2319:23, 8 May 2013 diff hist +61 Tools for protein and ligand analysis No edit summary
- 19:2019:20, 8 May 2013 diff hist +12 Dock Sampling →2. Calculate RMSD values for all orientations compared to the crystal structure pose
- 19:1919:19, 8 May 2013 diff hist +3,750 Dock Sampling No edit summary
- 18:2018:20, 8 May 2013 diff hist 0 N File:Nz14 xtal vs dock vs sampled.png No edit summary current
- 18:2018:20, 8 May 2013 diff hist 0 N File:Nz14 xtal vs dock.png No edit summary current
- 18:1918:19, 8 May 2013 diff hist +474 Dock Sampling No edit summary
- 18:1318:13, 8 May 2013 diff hist +763 N Dock Sampling Created page with "=Pose Sampling in DOCK= Don't get right DOCK pose? Well, this happens a lot... Docking is a complicated process, but it can be broken down to two main processes: scoring and ..."
- 18:0818:08, 8 May 2013 diff hist +9 Tutorials No edit summary
- 18:0018:00, 8 May 2013 diff hist −24 Tools for protein and ligand analysis No edit summary
- 00:0900:09, 8 May 2013 diff hist +53 FlexPepDock →Acknowlegements
7 May 2013
- 23:4623:46, 7 May 2013 diff hist +237 FlexPepDock No edit summary
- 23:4123:41, 7 May 2013 diff hist +1,481 FlexPepDock No edit summary
- 23:2323:23, 7 May 2013 diff hist 0 N File:Pose1 input output vs xray.png No edit summary current
- 23:2223:22, 7 May 2013 diff hist 0 N File:Rec w output peptides.png No edit summary current
- 23:2223:22, 7 May 2013 diff hist 0 N File:Rec w input peptides.png No edit summary current
- 23:2123:21, 7 May 2013 diff hist 0 N File:Rec w arg327.png No edit summary current
- 23:1823:18, 7 May 2013 diff hist +147 Tutorials No edit summary
- 23:1223:12, 7 May 2013 diff hist +11 FlexPepDock No edit summary
- 23:1123:11, 7 May 2013 diff hist +47 FlexPepDock No edit summary
- 23:0823:08, 7 May 2013 diff hist +126 FlexPepDock No edit summary
- 23:0623:06, 7 May 2013 diff hist +1,210 FlexPepDock Undo revision 5500 by Oliv Eidam (talk)
- 22:0222:02, 7 May 2013 diff hist +14 FlexPepDock No edit summary
- 22:0022:00, 7 May 2013 diff hist +2,003 FlexPepDock No edit summary
- 18:1618:16, 7 May 2013 diff hist +1,573 FlexPepDock No edit summary
- 00:4300:43, 7 May 2013 diff hist +138 FlexPepDock No edit summary
- 00:2500:25, 7 May 2013 diff hist +246 FlexPepDock No edit summary
- 00:1400:14, 7 May 2013 diff hist +849 N FlexPepDock Created page with "=FlexPepDock: Wanna dock a peptide? Use FlexPepDock!= Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest ..."
6 May 2013
- 23:3723:37, 6 May 2013 diff hist +91 Calculate DOCK6 RMSD No edit summary
- 23:3423:34, 6 May 2013 diff hist +65 Phenix No edit summary
- 23:3323:33, 6 May 2013 diff hist +79 Screen3d No edit summary
- 23:3223:32, 6 May 2013 diff hist −8 Omega.parm →Acknowledgments
- 23:3223:32, 6 May 2013 diff hist +51 Omega.parm No edit summary
- 23:3123:31, 6 May 2013 diff hist +42 Plop No edit summary
- 23:3023:30, 6 May 2013 diff hist +90 Filter.py: No edit summary
- 23:0523:05, 6 May 2013 diff hist +383 Filter.py: No edit summary
- 22:5822:58, 6 May 2013 diff hist 0 N File:Piperidine opioid coords.png No edit summary current
- 22:5422:54, 6 May 2013 diff hist +2,893 N Filter.py: Created page with "=Filter.py: search a substructure in DOCK poses and calculate atom distances= Sometimes it is interesting to search for a substructure in your DOCK output poses and calculate..."
- 22:0322:03, 6 May 2013 diff hist −118 Calculate DOCK6 RMSD No edit summary
- 21:4821:48, 6 May 2013 diff hist +849 Screen3d No edit summary
- 21:4421:44, 6 May 2013 diff hist +1 Omega.parm No edit summary
- 21:4321:43, 6 May 2013 diff hist +20 Omega.parm No edit summary
- 21:4121:41, 6 May 2013 diff hist +1,019 Omega.parm No edit summary
- 21:3321:33, 6 May 2013 diff hist 0 N File:Omega1.png No edit summary current
- 21:3221:32, 6 May 2013 diff hist 0 N File:Dock4 noEstat.png No edit summary current
- 21:2321:23, 6 May 2013 diff hist +4 Plop No edit summary
- 21:1821:18, 6 May 2013 diff hist +886 Plop No edit summary
- 21:0821:08, 6 May 2013 diff hist +249 Plop No edit summary
- 21:0821:08, 6 May 2013 diff hist 0 N File:Map.png No edit summary current
- 21:0721:07, 6 May 2013 diff hist 0 N File:Plop960.png No edit summary current
- 21:0721:07, 6 May 2013 diff hist 0 N File:Xtal.png No edit summary current
30 April 2013
- 23:5523:55, 30 April 2013 diff hist +1 Phenix No edit summary
- 23:5423:54, 30 April 2013 diff hist 0 N File:Sa omit map2.png No edit summary current
- 23:4423:44, 30 April 2013 diff hist +13 Phenix No edit summary
- 23:3823:38, 30 April 2013 diff hist +1,201 Phenix No edit summary
- 23:3023:30, 30 April 2013 diff hist 0 N File:Sa omit map.png No edit summary current
- 23:1823:18, 30 April 2013 diff hist +1,019 Phenix No edit summary
- 20:4020:40, 30 April 2013 diff hist +487 Phenix No edit summary
- 18:2818:28, 30 April 2013 diff hist 0 N File:Pdb sf download.jpg No edit summary current
- 18:2118:21, 30 April 2013 diff hist +577 N Phenix Created page with "==Calculate electron densities using Phenix== Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at el..."
29 April 2013
- 22:5222:52, 29 April 2013 diff hist +19 Calculate DOCK6 RMSD No edit summary
- 22:5022:50, 29 April 2013 diff hist +3,005 N Calculate DOCK6 RMSD Created page with "==Calculate ligand RMSDs using DOCK6== Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well. All you need is two ligands (with the same number of atoms..."
- 22:0822:08, 29 April 2013 diff hist +4 Tools for protein and ligand analysis No edit summary
- 22:0722:07, 29 April 2013 diff hist +2,855 N Omega.parm Created page with "==Changing settings for OMEGA (OpenEye)== You may be interested to change the default settings for OMEGA (defined in omega.py) when generating conformations for docking. Maby..."
- 22:0422:04, 29 April 2013 diff hist +145 Omega.py No edit summary
- 22:0022:00, 29 April 2013 diff hist −1,654 Omega.py No edit summary
- 21:4921:49, 29 April 2013 diff hist +495 Screen3d No edit summary
- 20:3820:38, 29 April 2013 diff hist +1,703 N Screen3d Created page with "==Sceen3d: Align ligands in 3D== This tool is useful if you want to align (superpose) conformations of a ligand (for example generated by OMEGA). Maybe you are interested to ..."
26 April 2013
- 23:4023:40, 26 April 2013 diff hist +68 Omega.py No edit summary
- 22:4222:42, 26 April 2013 diff hist +4,296 N Omega.py Created page with "==Changing settings for Omega (OpenEye)== You may be interested to change the default settings for Omega (defined in omega.py) when generating conformations for docking. Maby..."
- 19:0819:08, 26 April 2013 diff hist +156 Plop No edit summary
- 19:0319:03, 26 April 2013 diff hist +12 Plop No edit summary
- 19:0319:03, 26 April 2013 diff hist +6 Plop No edit summary
25 April 2013
- 21:3021:30, 25 April 2013 diff hist 0 Plop No edit summary
- 21:2621:26, 25 April 2013 diff hist 0 Plop No edit summary
- 21:2421:24, 25 April 2013 diff hist −40 Plop No edit summary
- 21:2321:23, 25 April 2013 diff hist +1 Plop No edit summary
- 21:2321:23, 25 April 2013 diff hist +322 Plop No edit summary
- 21:1521:15, 25 April 2013 diff hist −1 Plop No edit summary
- 21:1421:14, 25 April 2013 diff hist +276 Plop No edit summary
- 21:0821:08, 25 April 2013 diff hist +80 Plop No edit summary
- 21:0621:06, 25 April 2013 diff hist +2,908 N Plop Created page with "==Energy minimization using Plop== This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br> Check also the Plop manual on the Jaco..."
18 April 2013
- 23:4523:45, 18 April 2013 diff hist +643 Tools for protein and ligand analysis No edit summary
- 18:1418:14, 18 April 2013 diff hist +71 Tools for protein and ligand analysis No edit summary
- 18:1118:11, 18 April 2013 diff hist −5 Tools for protein and ligand analysis No edit summary
- 18:1118:11, 18 April 2013 diff hist −2 Tools for protein and ligand analysis No edit summary
- 18:0818:08, 18 April 2013 diff hist +76 N Tools for protein and ligand analysis Created page with "- Plop - omega.py - screen3d - Phenix - filter.py - FlexPepDock - DOCK6 RMSD"