http://wiki.docking.org/api.php?action=feedcontributions&feedformat=atom&user=BbenderDISI - User contributions [en]2026-05-24T00:43:10ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=DOCK_3.7&diff=12961DOCK 3.72020-09-23T14:55:46Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Tutorials =<br />
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
<br />
= Prepare Receptor = <br />
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''<br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
'''These scripts are also out of date. Where is setup_zinc15_file_number.py for LSD?'''<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)<br />
* [[How to process results from a large-scale docking]] : contains the blazing fast scripts for LSD processing<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12960DOCK 3.72020-09-23T14:51:59Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Tutorials =<br />
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
<br />
= Prepare Receptor = <br />
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''<br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
'''These scripts are also out of date. Where is setup_zinc15_file_number.py and variations?'''<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12959DOCK 3.72020-09-23T14:51:00Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Tutorials =<br />
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
<br />
= Prepare Receptor = <br />
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''<br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
'''These scripts are also out of date. Where is setup_zinc15_file_number.py and variations?'''<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12958DOCK 3.72020-09-23T14:48:47Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Tutorials =<br />
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
<br />
= Prepare Receptor = <br />
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''<br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12957DOCK 3.72020-09-23T14:46:40Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Tutorials =<br />
These are getting quite old, need updating<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
<br />
= Prepare Receptor = <br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12956DOCK 3.72020-09-23T14:00:58Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Prepare Receptor = <br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)<br />
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster<br />
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere<br />
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12955DOCK 3.72020-09-23T13:58:35Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Prepare Receptor = <br />
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]]<br />
* [[How to do parameter scanning]]<br />
*[[Matching Sphere Scan]]<br />
*[[Removing Spheres (The Chase Method)]]<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12954DOCK 3.72020-09-23T13:54:35Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Prepare Receptor = <br />
* [[Protein Target Preparation]]<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]]<br />
* [[How to do parameter scanning]]<br />
*[[Matching Sphere Scan]]<br />
*[[Removing Spheres (The Chase Method)]]<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=DOCK_3.7&diff=12953DOCK 3.72020-09-23T13:53:53Z<p>Bbender: </p>
<hr />
<div>= About = <br />
<br />
DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br />
protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br />
<br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
{{TOCright}}<br />
<br />
= Start here =<br />
* [[So you want to set up a lab]] - only if you don't already have hardware ready.<br />
* [[Install DOCK 3.7]]<br />
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br />
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br />
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br />
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)]]<br />
* [[DOCK 3.7 tutorial (Anat)]]<br />
* [[DOCK 3.7 with GIST tutorials]]<br />
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br />
* [[Getting started with DOCK 3.7]]<br />
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]].<br />
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br />
* [[Ligand preparation]] - different version. <br />
* [[Ligand prep Irwin Nov 2016]] - John's current version<br />
* [[Mol2db2 Format 2]] - details on the database formate.<br />
* [[Running docking 3.7]] - how to actually run docking.<br />
* [[DOCK 3.7 Development]] - for software developers<br />
* [[prepare a receptor with a cofactor for docking]]<br />
=== For DOCKovalent, start here ===<br />
* [[DOCKovalent_3.7]]<br />
* [[DOCKovalent lysine inhibitor design tutorial]]<br />
* [[DOCKovalent cysteine inhibitor design tutorial]]<br />
<br />
= Prepare Receptor = <br />
* [[Protein Target Preparation]]<br />
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster<br />
* [[Using_thin_spheres_in_DOCK3.7]]<br />
* [[How to do parameter scanning]]<br />
*[[Matching Sphere Scan]]<br />
*[[Removing Spheres (The Chase Method)]]<br />
* [[Adding Static Waters to the Protein Structure]]<br />
* [[Flexible Docking]]<br />
* [[Visualize docking grids]]<br />
* [[Minimize protein-ligand complex with AMBER]]<br />
* [[Minimize protein-covalent ligand complex with AMBER]]<br />
<br />
= Prepare Screening Library =<br />
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br />
* [[ligand preparation 3.7]]<br />
* [[generating decoys (Reed's way)]]<br />
* [[generating extrema set]]<br />
<br />
= Running Docking =<br />
* [[Running docking 3.7]] - JJI currently working on this.<br />
* [[Running DOCK 3.7]] - this seems to be slightly dated.<br />
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br />
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br />
* Interpreting the [[OUTDOCK 3.7]] file.<br />
<br />
= Analysis =<br />
* [[Analyzing DOCK Results]]<br />
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br />
* [[Other Useful Stuff]]<br />
* [[Bootstrap AUC]]<br />
* [[another getposes.py]]<br />
* [[Converting SMILES to Kekule Format]]<br />
* Viewing results using [[ViewDock]]<br />
<br />
= Post Docking Clustering=<br />
* [[How to process results from a large-scale docking]] <br />
* [[Large-scale SMILES Requesting and Fingerprints Converting]]<br />
* [[ECFP4 Best First Clustering]]<br />
* [[Bemis-Murcko Scaffold Analysis]]<br />
<br />
= Post Docking Filters=<br />
* [[Large-scale TC Calculations]]<br />
* [[Whole Library TC to Knowns Calculations]]<br />
* [[Filtering ligands for novelty]]<br />
* [[Strain Filtering]]<br />
* [[Interaction Filtering]]<br />
* [[Torsion against CSD visualize with Maestro]]<br />
<br />
= Redocking with Enhanced Sampling =<br />
*[[Sample Additional Ring Puckers ]]<br />
= Rescoring =<br />
*[[Rescoring_with_DOCK_3.7]]<br />
<br />
= Available Libraries = <br />
* [[ZINC Subset DB2 file locations]]<br />
* how to get db2 files from zinc15.docking.org<br />
<br />
= Analog by Catalog= <br />
* [[Substructure searching]]<br />
* [[TC analog searching in ZINC]]<br />
<br />
= Previous verisons and compatibility = <br />
DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br />
which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br />
<br />
= How to Cite = <br />
To cite the DOCK 3.7 paper, please use<br />
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]<br />
<br />
= How to Download = <br />
DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br />
<br />
= How to Setup a Slurm node = <br />
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm<br />
<br />
= Implementation = <br />
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br />
<br />
{{Template:CC-BY-SA-30}}<br />
{{Template:Coleman}}<br />
<br />
[[Category:DOCK 3.7]]<br />
[[Category:Software]]<br />
[[Category:Freecom]]</div>Bbenderhttp://wiki.docking.org/index.php?title=Covid19&diff=12321Covid192020-03-17T16:37:01Z<p>Bbender: </p>
<hr />
<div>Single landing page for lab procedures affected by the campus closure due to Covid19.<br />
<br />
<br />
== Guidance from BKS ==<br />
<br />
Both UCSF and the new SF ordinance allow for skeleton crew to be on site to take care of urgent business. They direct us to follow social distancing, wear gloves, minimize your time in contact with people. If someone from the city (e.g., the police) or UCSF asks, that is your (legitimate!) explanation.<br />
<br />
But we can receive and even redirect packages onward. <br />
<br />
For compounds destined for UNC, I suggest they stay here at UCSF, stored appropriately; UNC is shutting down too. Covid-19 molecules should still be sent on to Paris and NYC.<br />
<br />
I have designated four lab folks as crucial with permission to be on site after Wednesday: John, me, Parnian and JK. I have discussed this with UCSF emergency response.<br />
<br />
Please remember to refresh the google doc with your status. Every couple of days at least, even every day. Its important not just for you but everyone. <br />
<br />
<br />
== Important Questions ==<br />
1. Has everyone been successful logging in remotely? Are your public ssh keys working with gimel/portal? Are you trying to get remote desktops like Teamviewer working?<br />
Please add suggestions on making work from home easier.<br />
<br />
2. Do you have a package being delivered? Can it be held by the company (Genscript is offering this)? If it is coming to UCSF, can it sit at room temp or does it need to be stored in the freezer/fridge? Who handles this?<br />
<br />
3. What about meetings? Does everyone have Zoom access/Skype?<br />
Suggestion: for subgroup meetings, we do a shared google slides like the Roth lab meeting<br />
<br />
4. Hardware/computation issues: "I'm having problems with gimel, my workstation, need software installed, computer needs a reboot, etc." Who do I contact?<br />
<br />
5. Technical help: "I need help debugging a script, does any have a script that does X, etc.". How do we maintain contact with labmates?<br />
Suggestion: this is a perfect use-case for Slack, large group debugging, individual assistance, lab announcements, etc. Google hangouts and email viable but less organized. <br />
<br />
6. Maybe a weekly virtual coffee hour/beer hour to stay connected socially as well.</div>Bbenderhttp://wiki.docking.org/index.php?title=Covid19&diff=12320Covid192020-03-17T16:36:39Z<p>Bbender: </p>
<hr />
<div>Single landing page for lab procedures affected by the campus closure due to Covid19.<br />
<br />
<br />
== Guidance from BKS ==<br />
<br />
Both UCSF and the new SF ordinance allow for skeleton crew to be on site to take care of urgent business. They direct us to follow social distancing, wear gloves, minimize your time in contact with people. If someone from the city (e.g., the police) or UCSF asks, that is your (legitimate!) explanation.<br />
<br />
But we can receive and even redirect packages onward. <br />
<br />
For compounds destined for UNC, I suggest they stay here at UCSF, stored appropriately; UNC is shutting down too. Covid-19 molecules should still be sent on to Paris and NYC.<br />
<br />
I have designated four lab folks as crucial with permission to be on site after Wednesday: John, me, Parnian and JK. I have discussed this with UCSF emergency response.<br />
<br />
Please remember to refresh the google doc with your status. Every couple of days at least, even every day. Its important not just for you but everyone. <br />
<br />
<br />
== Important Questions ==<br />
1. Has everyone been successful logging in remotely? Are your public ssh keys working with gimel/portal? Are you trying to get remote desktops like Teamviewer working?<br />
Please add suggestions on making work from home easier.<br />
<br />
2. Do you have a package being delivered? Can it be held by the company (Genscript is offering this)? If it is coming to UCSF, can it sit at room temp or does it need to be stored in the freezer/fridge? Who handles this?<br />
<br />
3. What about meetings? Does everyone have Zoom access/Skype?<br />
Suggestion: for subgroup meetings, we do a shared google slides like the Roth lab meeting<br />
<br />
4. Hardware/computation issues: "I'm having problems with gimel, my workstation, need software installed, computer needs a reboot, etc." Who do I contact?<br />
<br />
5. Technical help: "I need help debugging a script, does any have a script that does X, etc.". How do we maintain contact with labmates?<br />
Suggestion: this is a perfect use-case for Slack, large group debugging, individual assistance, lab announcements, etc. Google hangouts and email viable but less organized. Maybe a weekly virtual coffee hour/beer hour to stay connected socially as well.</div>Bbenderhttp://wiki.docking.org/index.php?title=Covid19&diff=12319Covid192020-03-17T16:30:44Z<p>Bbender: </p>
<hr />
<div>Single landing page for lab procedures affected by the campus closure due to Covid19.<br />
<br />
<br />
== Guidance from BKS ==<br />
<br />
Both UCSF and the new SF ordinance allow for skeleton crew to be on site to take care of urgent business. They direct us to follow social distancing, wear gloves, minimize your time in contact with people. If someone from the city (e.g., the police) or UCSF asks, that is your (legitimate!) explanation.<br />
<br />
But we can receive and even redirect packages onward. <br />
<br />
For compounds destined for UNC, I suggest they stay here at UCSF, stored appropriately; UNC is shutting down too. Covid-19 molecules should still be sent on to Paris and NYC.<br />
<br />
I have designated four lab folks as crucial with permission to be on site after Wednesday: John, me, Parnian and JK. I have discussed this with UCSF emergency response.<br />
<br />
Please remember to refresh the google doc with your status. Every couple of days at least, even every day. Its important not just for you but everyone. <br />
<br />
<br />
== Important Questions ==<br />
1. Has everyone been successful logging in remotely? Are your public ssh keys working with gimel/portal? Are you trying to get remote desktops like Teamviewer working?<br />
Please add suggestions on making work from home easier.<br />
<br />
2. Do you have a package being delivered? Can it be held by the company (Genscript is offering this)? If it is coming to UCSF, can it sit at room temp or does it need to be stored in the freezer/fridge? Who handles this?<br />
<br />
3. What about meetings? Does everyone have Zoom access/Skype?<br />
Suggestion: for subgroup meetings, we do a shared google slides like the Roth lab meeting<br />
<br />
4. Hardware/computation issues: "I'm having problems with gimel, my workstation, need software installed, computer needs a reboot, etc." Who do I contact?<br />
<br />
5. Technical help: "I need help debugging a script, does any have a script that does X, etc.". How do we maintain contact with labmates?<br />
Suggestion: this is a perfect use-case for Slack, large group debugging, individual assistance, lab announcements, etc. Google hangouts and email viable but less organized.</div>Bbenderhttp://wiki.docking.org/index.php?title=Covid19&diff=12318Covid192020-03-17T16:27:09Z<p>Bbender: Created page with "Single landing page for lab procedures affected by the campus closure due to Covid19. == Guidance from BKS == Both UCSF and the new SF ordinance allow for skeleton crew to ..."</p>
<hr />
<div>Single landing page for lab procedures affected by the campus closure due to Covid19.<br />
<br />
<br />
== Guidance from BKS ==<br />
<br />
Both UCSF and the new SF ordinance allow for skeleton crew to be on site to take care of urgent business. They direct us to follow social distancing, wear gloves, minimize your time in contact with people. If someone from the city (e.g., the police) or UCSF asks, that is your (legitimate!) explanation.<br />
<br />
But we can receive and even redirect packages onward. <br />
<br />
For compounds destined for UNC, I suggest they stay here at UCSF, stored appropriately; UNC is shutting down too. Covid-19 molecules should still be sent on to Paris and NYC.<br />
<br />
I have designated four lab folks as crucial with permission to be on site after Wednesday: John, me, Parnian and JK. I have discussed this with UCSF emergency response.<br />
<br />
Please remember to refresh the google doc with your status. Every couple of days at least, even every day. Its important not just for you but everyone. <br />
<br />
<br />
== Important Questions ==<br />
1. Has everyone been successful logging in remotely? Are your public ssh keys working with gimel/portal? Are you trying to get remote desktops like Teamviewer working?<br />
Please add suggestions on making work from home easier.<br />
<br />
2. Do you have a package being delivered? Can it be held by the company (Genscript is offering this)? If it is coming to UCSF, can it sit at room temp or does it need to be stored in the freezer/fridge? Who handles this?<br />
<br />
3. What about meetings? Does everyone have Zoom access/Skype?<br />
Suggestion: for subgroup meetings, we do a shared google slides like the Roth lab meeting</div>Bbender