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
- 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- DOCK 3.7 2015/04/15 abl1 Tutorial superseded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
- Blastermaster - Prepare input for and then run DOCK 3.7.
- 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
Prepare Receptor
- 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
- Flexible Docking
- Visualize docking grids
- Minimize protein-ligand complex with AMBER
- Minimize protein-covalent ligand complex with AMBER
Prepare Screening Library
- 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
- 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
- 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
Rescoring
Available Libraries
- ZINC Subset DB2 file locations
- how to get db2 files from zinc15.docking.org
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 node step-by-step 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/.