DOCK 3.7

About

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/. It is the latest version in the DOCK 3 series of docking programs developed and used by the Shoichet Lab. To cite the DOCK 3.7 paper, please use 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, written in a variety of languages. It comes with some tools necessary to build ligands, though some tools are under commercial/free academic license that must be obtained externally. It uses new Flexibase/DB2 files found on ZINC (eventually). It includes tools to prepare receptors, written in a variety of languages, and several auxiliary scripts written in Python.

Start here

• So you want to set up a lab
• Install DOCK 3.7
• DOCK 3.7 2014/09/25 FXa Tutorial
• 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.
• 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 Receptor

• Protein Target Preparation
• Adding Static Waters to the Protein Structure
• Flexible Docking

Prepare Screening Library

• mol2db2 is the program that creates mol2db2 format database files which are read by DOCK 3.7
• ligand preparation 3.7

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
• Interpreting the OUTDOCK 3.7 file.

Analysis

• Analyzing DOCK Results
• Auto-DUD-E Test Set (external site)

Available Libraries

• ZINC Subset DB2 file locations

Previous verisons

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.

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/.

Programming Language

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

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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/.