User contributions
Jump to navigation
Jump to search
- 22:46, 17 March 2021 diff hist +2,194 How to dock in DOCK3.8
- 19:12, 12 March 2021 diff hist +3 AutoQSAR/DeepChem for billions of molecules current
- 19:12, 12 March 2021 diff hist +62 AutoQSAR/DeepChem for billions of molecules
- 19:11, 12 March 2021 diff hist -7 AutoQSAR/DeepChem for billions of molecules
- 19:10, 12 March 2021 diff hist +12 AutoQSAR/DeepChem for billions of molecules
- 19:09, 12 March 2021 diff hist +69 AutoQSAR/DeepChem for billions of molecules
- 19:01, 12 March 2021 diff hist 0 AutoQSAR/DeepChem for billions of molecules →Analyze prediction
- 19:01, 12 March 2021 diff hist 0 AutoQSAR/DeepChem for billions of molecules →Analyze prediction
- 19:00, 12 March 2021 diff hist +1 AutoQSAR/DeepChem for billions of molecules
- 19:00, 12 March 2021 diff hist +52 AutoQSAR/DeepChem for billions of molecules
- 18:59, 12 March 2021 diff hist +5,486 AutoQSAR/DeepChem for billions of molecules
- 17:56, 12 March 2021 diff hist 0 N File:Figure dockscore for ML.png current
- 18:03, 11 March 2021 diff hist +41 How to dock in DOCK3.8
- 17:59, 11 March 2021 diff hist +1 How to dock in DOCK3.8
- 05:56, 11 March 2021 diff hist +105 How to dock in DOCK3.8
- 05:53, 11 March 2021 diff hist +7 How to dock in DOCK3.8
- 05:53, 11 March 2021 diff hist +36 How to dock in DOCK3.8
- 05:52, 11 March 2021 diff hist +8 How to dock in DOCK3.8
- 05:50, 11 March 2021 diff hist +1,803 How to dock in DOCK3.8
- 23:42, 8 March 2021 diff hist +143 FEP+ for GPCR
- 23:40, 8 March 2021 diff hist +67 FEP+ for GPCR
- 23:35, 8 March 2021 diff hist +71 FEP+ for GPCR
- 22:44, 8 March 2021 diff hist -23 FEP+ for GPCR
- 22:28, 8 March 2021 diff hist 0 FEP+ for GPCR
- 22:28, 8 March 2021 diff hist 0 FEP+ for GPCR
- 22:27, 8 March 2021 diff hist 0 N File:SID analysis.png current
- 22:27, 8 March 2021 diff hist +109 FEP+ for GPCR
- 22:16, 8 March 2021 diff hist +979 FEP+ for GPCR
- 22:02, 8 March 2021 diff hist +38 FEP+ for GPCR
- 21:40, 26 February 2021 diff hist +2 FEP+ for GPCR
- 21:40, 26 February 2021 diff hist +5 FEP+ for GPCR
- 21:39, 26 February 2021 diff hist -7 FEP+ for GPCR
- 18:58, 26 February 2021 diff hist -15 DOCK 3.7 →FEP+ and AutoQSAR/DeepChem with Schrodinger Suites
- 18:57, 26 February 2021 diff hist -16 AutoQSAR/DeepChem for billions of molecules
- 18:56, 26 February 2021 diff hist +210 N AutoQSAR/DeepChem for billions of molecules Created page with "2/25/2021 Ying Yang 1. Train a ML model based on smiles and scores (dock scores / FEP predicted values) 2. Apply the ML model to predict all molecules (smiles) of interest 3..."
- 18:54, 26 February 2021 diff hist +273 FEP+ for GPCR
- 18:51, 26 February 2021 diff hist +19 FEP+ for GPCR
- 18:51, 26 February 2021 diff hist -19 FEP+ for GPCR
- 18:50, 26 February 2021 diff hist +143 FEP+ for GPCR
- 18:48, 26 February 2021 diff hist 0 N File:Workflow FEP.png current
- 18:48, 26 February 2021 diff hist +232 N FEP+ for GPCR Created page with "2/25/2021 Ying Yang Steps for setting up a FEP prediction for membrane protein * Equilibration of complex structure (with confident binding pose) * Force field builder ..."
- 18:32, 26 February 2021 diff hist +126 DOCK 3.7
- 04:30, 22 October 2020 diff hist +493 N Calculate RMSD between two sets of molecules (eg, Crystal pose vs. docked pose) Created page with "10/21/2020 Ying Script to calculate RMSD between two sets of molecules (mol2 format), modified from the openeye rmsd.py (https://docs.eyesopen.com/toolkits/python/_downloads/..." current
- 04:22, 22 October 2020 diff hist 0 Other Useful Stuff current
- 04:21, 22 October 2020 diff hist +88 Other Useful Stuff
- 05:45, 6 October 2020 diff hist 0 Another getposes.py current
- 05:44, 6 October 2020 diff hist +504 Another getposes.py
- 21:54, 5 August 2020 diff hist +65 Interaction Filtering
- 21:54, 5 August 2020 diff hist 0 N File:2d html.png current
- 21:52, 5 August 2020 diff hist +1 Interaction Filtering
- 21:52, 5 August 2020 diff hist +384 Interaction Filtering
- 20:01, 15 May 2020 diff hist -13 Torsion against CSD visualize with Maestro current
- 19:58, 15 May 2020 diff hist +595 Torsion against CSD visualize with Maestro
- 19:48, 15 May 2020 diff hist 0 N File:Maestro csd pic4.png current
- 19:48, 15 May 2020 diff hist 0 N File:Maestro csd pic3.png current
- 19:48, 15 May 2020 diff hist 0 N File:Maestro csd pic2.png current
- 19:48, 15 May 2020 diff hist 0 N File:Maestro csd pic1.png current
- 19:36, 15 May 2020 diff hist +536 N Torsion against CSD visualize with Maestro Created page with "5/15/2020 Ying Besides the automated strain filtering, it's useful to visualize the torsion angle in against CSD. Here's an example of how to do it with Schrodinger tools. ..."
- 17:35, 15 May 2020 diff hist +49 DOCK 3.7
- 04:47, 9 May 2020 diff hist +5 Another getposes.py
- 04:42, 9 May 2020 diff hist +290 Another getposes.py
- 07:03, 20 April 2020 diff hist +22 Another getposes.py
- 02:37, 20 April 2020 diff hist +2 Another getposes.py
- 02:37, 20 April 2020 diff hist +202 Another getposes.py
- 21:26, 31 March 2020 diff hist +42 Another getposes.py
- 21:24, 31 March 2020 diff hist +1,972 N Another getposes.py Created page with "3/25/2020 Ying Poses are needed for Shuo's interaction filter and strain filter, sometimes we need to get poses pre-clustering. Owing to the need, here's another get_poses.py..."
- 21:23, 31 March 2020 diff hist -1 DOCK 3.7
- 21:22, 31 March 2020 diff hist +1 DOCK 3.7
- 21:22, 31 March 2020 diff hist -1 DOCK 3.7
- 21:21, 31 March 2020 diff hist 0 N File:Runtime getposes.png current
- 01:19, 26 March 2020 diff hist +1 Another get poses.py current
- 01:18, 26 March 2020 diff hist +437 Bootstrap AUC current
- 01:13, 26 March 2020 diff hist +109 Bootstrap AUC
- 01:12, 26 March 2020 diff hist 0 N File:Bootstrap out logAUC.png current
- 01:12, 26 March 2020 diff hist 0 N File:Bootstrap out AUC.png current
- 01:09, 26 March 2020 diff hist +1,978 Bootstrap AUC
- 00:16, 25 March 2020 diff hist +465 Another get poses.py
- 00:03, 25 March 2020 diff hist +485 Another get poses.py
- 23:55, 24 March 2020 diff hist +768 N Another get poses.py Created page with "Another get_poses.py script modified on top of getposes_blazing_faster.py from Reed & Trent source /nfs/home/yingyang/.cshrc_opencadd python /nfs/home/yingyang/scripts/get_p..."
- 23:53, 24 March 2020 diff hist +27 DOCK 3.7
- 23:20, 25 February 2019 diff hist 0 File:Variation AUC logAUC.png Yingyang uploaded a new version of "File:Variation AUC logAUC.png" current
- 23:18, 25 February 2019 diff hist +148 Bootstrap AUC →Plot the change(s) in AUC/logAUC against reference score
- 23:16, 25 February 2019 diff hist 0 File:Fig compare methods.png Yingyang uploaded a new version of "File:Fig compare methods.png" current
- 23:15, 25 February 2019 diff hist +53 Bootstrap AUC →Plot the change(s) in AUC/logAUC against reference score
- 23:15, 25 February 2019 diff hist +19 Bootstrap AUC →Plot the variation of AUC/logAUC
- 23:14, 25 February 2019 diff hist -51 Bootstrap AUC →Plot the variation of AUC/logAUC
- 23:14, 25 February 2019 diff hist 0 N File:Fig compare methods.png
- 23:03, 25 February 2019 diff hist 0 N File:Variation AUC logAUC.png
- 23:03, 25 February 2019 diff hist +1,021 N Bootstrap AUC Created page with "To test whether the difference in AUC/logAUC between two methods is statistically significant or not, AUC/logAUC of the new developed method(s) against the reference method ca..."
- 22:17, 25 February 2019 diff hist +20 DOCK 3.7 →Analysis
