ViewDock TDW: high-throughput visualization of virtual screening results

Abstract

Summary: ViewDock TDW is a modification of the pre-existing ViewDock Chimera extension (http://www.cgl.ucsf.edu/chimera/) used to visualize results of virtual screening experiments. By combing TDW hardware and an enhanced ViewDock interface, dozens of ligand-protein complexes are rendered simultaneously to parallelize the analysis of candidate ligands. The ViewDock TDW GUI allows the user to easily and interactively manipulate the molecules on the TDW as an entire set, a selected subset or a single ligand-protein complex and preserves all Chimera functionality.

Availability and implementation: ViewDock TDW is an open source software; freely available on the web at http://www.tdw-prime.webs.com. Chimera UCSF is also available, free of charge, at http://www.cgl.ucsf.edu/chimera/

Fig. 1.

(A) Screenshot of ViewDock TDW GUI. Specific molecules are selected using the checkboxes on the bottom left of screenshot. The bottom right window demonstrates the ability to send commands via command line to the molecules in Chimera. (B) Picture of a 4 × 5 Tiled Wall Display. Twenty-four different candidate ligand–protein complexes are rendered simultaneously. The leftmost column of the TDW has two Chimera instances per display.