Difference between revisions of "DOCK 3.7"

From DISI
Jump to: navigation, search
m
 
(16 intermediate revisions by 3 users not shown)
Line 14: Line 14:
 
* [[So you want to set up a lab]] - only if you don't already have hardware ready.
 
* [[So you want to set up a lab]] - only if you don't already have hardware ready.
 
* [[Install DOCK 3.7]]
 
* [[Install DOCK 3.7]]
* [[DOCK 3.7 2014/09/25 FXa 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* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded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 tutorial (Anat)]]
 
* [[DOCK 3.7 with GIST tutorials]]
 
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]
 
 
* [[Getting started with DOCK 3.7]]
 
* [[Getting started with DOCK 3.7]]
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]].
+
* [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster
 
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].
 
* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].
 
* [[Ligand preparation]] - different version.  
 
* [[Ligand preparation]] - different version.  
Line 34: Line 27:
 
* [[DOCKovalent lysine inhibitor design tutorial]]
 
* [[DOCKovalent lysine inhibitor design tutorial]]
 
* [[DOCKovalent cysteine inhibitor design tutorial]]
 
* [[DOCKovalent cysteine inhibitor design tutorial]]
 +
 +
= Tutorials =
 +
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''
 +
* [[DOCK 3.7 2014/09/25 FXa 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* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded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 tutorial (Anat)]]
 +
* [[DOCK 3.7 with GIST tutorials]]
 +
* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]
  
 
= Prepare Receptor =  
 
= Prepare Receptor =  
* [[Protein Target Preparation]]
+
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''
* [[Protein Target Preparation Updated]]
+
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
* [[Using_thin_spheres_in_DOCK3.7]]
+
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
 +
* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)
 +
* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster
 +
*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere
 +
*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer
 
* [[Adding Static Waters to the Protein Structure]]
 
* [[Adding Static Waters to the Protein Structure]]
 
* [[Flexible Docking]]
 
* [[Flexible Docking]]
Line 46: Line 53:
  
 
= Prepare Screening Library =
 
= Prepare Screening Library =
 +
'''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'''
 
* [[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]]
Line 52: Line 60:
  
 
= Running Docking =
 
= Running Docking =
 +
'''These scripts are also out of date. Where is setup_zinc15_file_number.py for LSD?'''
 
* [[Running docking 3.7]] - JJI currently working on this.
 
* [[Running docking 3.7]] - JJI currently working on this.
 
* [[Running DOCK 3.7]] - this seems to be slightly dated.
 
* [[Running DOCK 3.7]] - this seems to be slightly dated.
Line 59: Line 68:
  
 
= Analysis =
 
= Analysis =
* [[Analyzing DOCK Results]]
+
* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)
 +
* [[How to process results from a large-scale docking]] : contains the blazing fast scripts for LSD processing
 
* [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]]
Line 104: Line 114:
 
= 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 06:55, 23 September 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

Tutorials

These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready

Prepare Receptor

These scripts setup the grids and matching spheres and are used to optimize the pocket

Prepare Screening Library

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

Running Docking

These scripts are also out of date. Where is setup_zinc15_file_number.py for LSD?

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/.