TY - JOUR
T1 - Accelerating virtual high-throughput ligand docking
T2 - Current technology and case study on a petascale supercomputer
AU - Ellingson, Sally R.
AU - Dakshanamurthy, Sivanesan
AU - Brown, Milton
AU - Smith, Jeremy C.
AU - Baudry, Jerome
PY - 2014/4/25
Y1 - 2014/4/25
N2 - In this paper, we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel Message Passing Interface version of AutoDock4 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 Message Passing Interface version of AutoDock4 are available online at http://www.bio.utk.edu/baudrylab/ autodockmpi.htm.
AB - In this paper, we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel Message Passing Interface version of AutoDock4 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 Message Passing Interface version of AutoDock4 are available online at http://www.bio.utk.edu/baudrylab/ autodockmpi.htm.
KW - automated molecular docking
KW - drug discovery
KW - high-performance computing
KW - virtual high-throughput screening
UR - https://www.scopus.com/pages/publications/84897065333
UR - https://www.scopus.com/pages/publications/84897065333#tab=citedBy
U2 - 10.1002/cpe.3070
DO - 10.1002/cpe.3070
M3 - Article
AN - SCOPUS:84897065333
SN - 1532-0626
VL - 26
SP - 1268
EP - 1277
JO - Concurrency and Computation: Practice and Experience
JF - Concurrency and Computation: Practice and Experience
IS - 6
ER -