Difference between revisions of "DOCK 3.7"

From DISI
Jump to: navigation, search
(Running Docking)
m (How to Setup a Slurm node)
 
(39 intermediate revisions by 9 users not shown)
Line 15: Line 15:
 
* [[Install DOCK 3.7]]
 
* [[Install DOCK 3.7]]
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]]
+
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded
 +
* [[DOCK 3.7 2018/06/05 abl1 Tutorial]]
 
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent &  Jiankun)]]
 
* [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent &  Jiankun)]]
 
* [[DOCK 3.7 tutorial (Anat)]]
 
* [[DOCK 3.7 tutorial (Anat)]]
Line 28: Line 29:
 
* [[Running docking 3.7]] - how to actually run docking.
 
* [[Running docking 3.7]] - how to actually run docking.
 
* [[DOCK 3.7 Development]] - for software developers
 
* [[DOCK 3.7 Development]] - for software developers
 +
* [[prepare a receptor with a cofactor for docking]]
 +
=== For DOCKovalent, start here ===
 +
* [[DOCKovalent_3.7]]
 +
* [[DOCKovalent lysine inhibitor design tutorial]]
 +
* [[DOCKovalent cysteine inhibitor design tutorial]]
  
 
= Prepare Receptor =  
 
= Prepare Receptor =  
 
* [[Protein Target Preparation]]
 
* [[Protein Target Preparation]]
 +
* [[Protein Target Preparation Updated]]
 +
* [[Using_thin_spheres_in_DOCK3.7]]
 +
* [[How to do parameter scanning]]
 +
*[[Matching Sphere Scan]]
 +
*[[Removing Spheres (The Chase Method)]]
 
* [[Adding Static Waters to the Protein Structure]]
 
* [[Adding Static Waters to the Protein Structure]]
 
* [[Flexible Docking]]
 
* [[Flexible Docking]]
 +
* [[Visualize docking grids]]
 +
* [[Minimize protein-ligand complex with AMBER]]
 +
* [[Minimize protein-covalent ligand complex with AMBER]]
  
 
= Prepare Screening Library =
 
= Prepare Screening Library =
 
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
 
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
 
* [[ligand preparation 3.7]]
 
* [[ligand preparation 3.7]]
 +
* [[generating decoys (Reed's way)]]
 +
* [[generating extrema set]]
  
 
= Running Docking =
 
= Running Docking =
Line 49: Line 65:
 
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)  
 
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)  
 
* [[Other Useful Stuff]]
 
* [[Other Useful Stuff]]
 +
* [[Bootstrap AUC]]
 +
* [[another getposes.py]]
 +
* [[Converting SMILES to Kekule Format]]
 +
* Viewing results using [[ViewDock]]
  
 
= Post Docking Clustering=
 
= Post Docking Clustering=
Line 58: Line 78:
 
= Post Docking Filters=
 
= Post Docking Filters=
 
* [[Large-scale TC Calculations]]
 
* [[Large-scale TC Calculations]]
 +
* [[Whole Library TC to Knowns Calculations]]
 +
* [[Filtering ligands for novelty]]
 +
* [[Strain Filtering]]
 +
* [[Interaction Filtering]]
 +
* [[Torsion against CSD visualize with Maestro]]
 +
 +
= Redocking with Enhanced Sampling =
 +
*[[Sample Additional Ring Puckers ]]
 +
= Rescoring =
 +
*[[Rescoring_with_DOCK_3.7]]
  
 
= Available Libraries =  
 
= Available Libraries =  
Line 65: Line 95:
 
= Analog by Catalog=  
 
= Analog by Catalog=  
 
* [[Substructure searching]]
 
* [[Substructure searching]]
 +
* [[TC analog searching in ZINC]]
  
 
= Previous verisons and compatibility =  
 
= Previous verisons and compatibility =  
Line 76: Line 107:
 
= How to Download =  
 
= How to Download =  
 
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 +
 +
= How to Setup a Slurm node =
 +
An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm
  
 
= Implementation =  
 
= Implementation =  

Latest revision as of 06:15, 27 May 2020

About

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 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.

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 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.

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/.

Start here

For DOCKovalent, start here

Prepare Receptor

Prepare Screening Library

Running Docking

Analysis

Post Docking Clustering

Post Docking Filters

Redocking with Enhanced Sampling

Rescoring

Available Libraries

Analog by Catalog

Previous verisons and compatibility

DOCK 3.7 is part of the DOCK 3 series. It differs substantially from its immediate predecessor DOCK 3.6, which uses a different format of database files that cannot be read by DOCK 3.7, and vice versa.

How to Cite

To cite the DOCK 3.7 paper, please use Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.

How to Download

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/.

How to Setup a Slurm node

An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm

Implementation

DOCK 3.7 is written in Fortran and some C. Scripts are mostly in python and perl.

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 this license, visit http://creativecommons.org/licenses/by-sa/3.0/ This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at https://sites.google.com/site/dock37wiki/.