DOCK 3.7

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.

Start here

• So you want to set up a lab
• Install DOCK 3.7
• 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.
• Running docking 3.7 - how to actually run docking.
• DOCK 3.7 Development - for software developers

Protein preparation for docking

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

Molecular library preparation for docking

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

Molecular 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 of Docking Results, including the use of decoys

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

Current cluster information pertaining to using DOCK 3.7

• 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.

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/.