Difference between revisions of "DOCK 3.7"

From DISI
Jump to: navigation, search
(Molecular library preparation for docking)
m
 
(89 intermediate revisions by 11 users not shown)
Line 1: Line 1:
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
+
= About =
It is the latest version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]].
+
 
To cite DOCK3.7 paper, please use
+
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
 
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]
 
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]
  
= Highest level scripts =
+
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/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 +
 
 
{{TOCright}}
 
{{TOCright}}
* [[Blastermaster]] - a program prepare input for and then run [[DOCK 3.7]], a molecular docking program.
+
 
* [[Ligand preparation 3.7]] - programs to create dockable databases
+
= Start here =
* [[Ligand preparation]] - somewhat different, apparently refers to versions on the UCSF/Toronto clusters, not in the distribution.  
+
* [[So you want to set up a lab]] - only if you don't already have hardware ready.
* [[Getting started with DOCK_3.7]] - notes by JJI, work in progress.
+
* [[Install DOCK 3.7]]
 +
* [[Getting started with 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]] - different version.  
 +
* [[Ligand prep Irwin Nov 2016]] - John's current version
 +
* [[Mol2db2 Format 2]] - details on the database formate.
 
* [[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
 +
* [[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]]
  
= Protein preparation for docking =  
+
= Tutorials =
* [[Protein Target Preparation]]
+
'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''
** [[Adding Static Waters to the Protein Structure]]
+
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
** [[Flexible Docking]]
+
* [[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]]
  
= Molecular library preparation for docking =
+
= Prepare Receptor =
 +
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''
 +
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
 +
* [[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]]
 +
* [[Flexible Docking]]
 +
* [[Visualize docking grids]]
 +
* [[Minimize protein-ligand complex with AMBER]]
 +
* [[Minimize protein-covalent ligand complex with AMBER]]
 +
 
 +
= 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]]
 +
* [[generating decoys (Reed's way)]]
 +
* [[generating extrema set]]
  
= Molecular docking =
+
= Running Docking =
* [[Running DOCK 3.7]]
+
'''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 DOCK 3.7]] - this seems to be slightly dated.
 
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]
 
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]
* Reading the [[OUTDOCK 3.7]] file.
+
* [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.
 +
* Interpreting the [[OUTDOCK 3.7]] file.
  
= Analysis of Docking Results, including the use of decoys =
+
= 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]]
 +
* [[Bootstrap AUC]]
 +
* [[another getposes.py]]
 +
* [[Converting SMILES to Kekule Format]]
 +
* Viewing results using [[ViewDock]]
  
= Current cluster information pertaining to using [[DOCK 3.7]] =  
+
= Post Docking Clustering=
 +
* [[How to process results from a large-scale docking]]
 +
* [[Large-scale SMILES Requesting and Fingerprints Converting]]
 +
* [[ECFP4 Best First Clustering]]
 +
* [[Bemis-Murcko Scaffold Analysis]]
 +
 
 +
= Post Docking Filters=
 +
* [[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 =  
 
* [[ZINC Subset DB2 file locations]]
 
* [[ZINC Subset DB2 file locations]]
 +
* how to get db2 files from zinc15.docking.org
 +
 +
= Analog by Catalog=
 +
* [[Substructure searching]]
 +
* [[TC analog searching in ZINC]]
 +
 +
= 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
 +
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]
 +
 +
= How to Download =
 +
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
  
= Previous verisons =  
+
= Implementation =  
DOCK 3.7 is part of the [[DOCK 3]] series. However, it differs substantially from its immediate predecessor [[DOCK 3.6]].  Importantly, [[DOCK 3.6]] uses a different format of database files that cannot be read by [[DOCK 3.7]] and vice versa.  
+
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].
  
 
{{Template:CC-BY-SA-30}}
 
{{Template:CC-BY-SA-30}}
Line 40: Line 125:
  
 
[[Category:DOCK 3.7]]
 
[[Category:DOCK 3.7]]
[[Category:DOCK]]
 
 
[[Category:Software]]
 
[[Category:Software]]
[[Category:Internal]]
+
[[Category:Freecom]]

Latest revision as of 07:55, 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/.