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Abstract
Molecular docking is widely used to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. Notwithstanding multiple attempts at automation, molecular docking continues to require the guidance of an expert thus limiting its use by many investigators who could benefit from it. To make docking more accessible we have created new software that allows us to investigate the automation of molecular docking screens. Our method currently requires known ligands and decoys for model evaluation. Of 42 DUDEZ targets, all show automated docking results that are better than our previous automated protocol. The new system is available both as part of the UCSF DOCK 3.8 package, which is free to academics, as well as via our website tldr.docking.org/start/dockopt (free registration required), which is free to everyone.
Supplementary materials
Title
Supporting information for DOCK Blaster 2.0 - An Investigation of Automated Docking
Description
S1. Online documentation about how to use DOCK Blaster 2.0
S2. Obtain, install and configure DOCK 3.8 on your computer.
S3. How to prepare a receptor and a ligand for docking.
S4. How to prepare actives.tgz and decoys.tgz for Dockopt
S5. A directed acyclic graph representing processes in DOCK Blaster
S6. Any step S is the union of several subgraphs T_i
S7. Example. How does allowing multiple parameters affect the graph?
S8. Example 2 : one version per vertex type (left) and same graph where two values are allowed for vertex v_1 (right)
S9. Post processing schematic.
S10. Improvement of Enrichment from the DUDEZ paper to dockopt optimization.
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