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Updated: May 1, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer
Sally R Ellingson1, Sivanesan Dakshanamurthy2, Milton Brown2
1Genome Science and Technology, University of Tennessee, Center for Molecular Biophysics, Oak Ridge National Laboratory.
Abstract:
In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.
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