DOCK 3.7

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

• So you want to set up a lab - only if you don't already have hardware ready.
• 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.
• 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

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• DOCK 3.7 2015/04/15 abl1 Tutorial superseded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

DOCK 3.8 Tutorials

• How to dock in DOCK3.8
• Docking Analysis in DOCK3.8

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
• Coloring and Subcluster Matching
• 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
• ligand preparation 3.7
• generating decoys (Reed's way)
• generating extrema set

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 DOCK 3.7 - this seems to be slightly dated.
• INDOCK 3.7 - file format used by DOCK 3.7
• 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

• 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
• Auto-DUD-E Test Set (external site)
• Other Useful Stuff
• Bootstrap AUC
• another getposes.py
• Converting SMILES to Kekule Format
• Viewing results using ViewDock

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
• how to get db2 files from zinc15.docking.org

Analog by Catalog

• Substructure searching
• TC analog searching in ZINC

FEP+ and ML with Schrodinger Suites

• FEP+ for GPCR
• AutoQSAR/DeepChem for billions of molecules

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/.