详细信息
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4
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PT
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Wolf, A Hofmann-Apitius, M Ghanem, M Azam, N Kalaitzopoulos, D Yu, KQ Kasam, V
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Wolf, Antje Hofmann-Apitius, Martin Ghanem, Moustafa Azam, Nabeel Kalaitzopoulos, Dimitrios Yu, Kunqian Kasam, Vinod
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DockFlow - a prototypic PharmaGrid for Virtual Screening Integrating Four Different Docking Tools
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HEALTHGRID RESEARCH, INNOVATION AND BUSINESS CASE
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English
DT
Proceedings Paper
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7th Healthgrid Conference
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JUN 29-JUL 01, 2009
CL
Berlin, GERMANY
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DE
Virtual Screening; Molecular Docking; FlexX; AutoDock; DOCK; GAsDock; Workflows; Docking Database; Grid Computing
ID
PROTEIN-LIGAND DOCKING; OPEN GRID SERVICES; GENETIC ALGORITHM; FLEXIBLE DOCKING; DISCOVERY; PROGRAMS; DESIGN; WEB
AB
In this paper we present DockFlow, a prototypic version of a PharmaGrid DockFlow is supporting pharmaceutical research through enabling virtual screening on the Grid The system was developed in the course of the BRIDGE project funded by the European Commission Grids have been used before to run compute- and data-intensive virtual screening experiments, like in the WISDOM project With DockFlow, however, we addressed a variety of problems yet unsolved, like the diversity of results produced by different docking tools We also addressed the problem of analysing the data produced in a distributed virtual screening system applying a combinatorial docking approach In DockFlow we worked on a grid-based problem solving environment for virtual screening with the following major features execution of four different docking services (FlexX, AutoDock, DOCK and GAsDock) at locations in Europe and China remotely from a common workflow, storage of the results in a common Docking Database providing a shared analysis platform for the collaboration partners and combination of the results The DockFlow prototype is evaluated on two scientific case studies malaria and avian flu
C1
1 [Wolf, Antje] Fraunhofer Inst Algorithms & Sci Comp SCAI, Dept Bioinformat, D-53754 St Augustin, Germany.
RP
Wolf, A, Fraunhofer Inst Algorithms & Sci Comp SCAI, Dept Bioinformat, D-53754 St Augustin, Germany.
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*GRIA, SERV OR COLL IND COM ALSAIRAFI S, 2003, INT J HIGH PERFORM C, V17, P297 ATKINSON M, 2005, CONCURR COMP-PRACT E, V17, P377, DOI 10.1002/cpe.936 BRETON V, 2005, ST HEAL T, V112, P249 CASE DA, 2005, J COMPUT CHEM, V26, P1668, DOI 10.1002/jcc.20290 CLAUSSEN H, 2004, CURR DRUG DISCOV TEC, V1, P49 COLE JC, 2005, PROTEINS, V60, P325, DOI 10.1002/prot.20497 CONGREVE M, 2005, DRUG DISCOV TODAY, V10, P895 EWING TJA, 2001, J COMPUT AID MOL DES, V15, P411 FOSTER I, 2002, OPEN GRID SERVICE IN FOSTER I, 2005, SCIENCE, V308, P814, DOI 10.1126/science.1110411 JIANG ZR, 2006, J DRUG TARGET, V14, P623, DOI 10.1080/10611860600866971 JONES G, 1997, J MOL BIOL, V267, P727 KASAM V, 2007, J CHEM INF MODEL, V47, P1818, DOI 10.1021/ci600451t KELLENBERGER E, 2004, PROTEINS, V57, P225, DOI 10.1002/prot.20149 KRAUTER K, 2002, SOFTWARE PRACT EXPER, V32, P135 LI HL, 2004, BIOORG MED CHEM LETT, V14, P4671, DOI 10.1016/j.bmcl.2004.06.091 MORRIS GM, 1998, J COMPUT CHEM, V19, P1639 PAUL N, 2002, PROTEINS, V47, P521 RAREY M, 1996, J MOL BIOL, V261, P470 ROWE A, 2003, BIOINFORMATICS, V19, P225 SCHULZGASCH T, 2003, J MOL MODEL, V9, P47, DOI 10.1007/s00894-002-0112-y SOUSA SF, 2006, PROTEINS, V65, P15, DOI 10.1002/prot.21082 SURRIDGE M, 2005, ESCIENCE 05 P 1 INT, P98 TALIA D, 2002, IEEE INTERNET COMPUT, V6, P67 WU Y, 2007, INT J WEB GRID SERV, V3, P371
NR
26
TC
0
PU
I O S PRESS
PI
AMSTERDAM
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NIEUWE HEMWEG 6B, 1013 BG AMSTERDAM, NETHERLANDS
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0926-9630
J9
9 ST HEAL T
JI
PD
PY
2009
VL
147
IS
BP
3
EP
12
DI
10.3233/978-1-60750-027-8-3
PG
10
SC
Health Care Sciences & Services; Medical Informatics
GA
BQK80
UT
ISI:000281217700002
ED
Solomonides, T; HofmannApitius, M; Freudigmann, M; Semler, SC; Legre, Y; Kratz, M
SU
BN
978-1-60750-027-8
SE
Studies in Health Technology and Informatics
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SI
AR
GP
PN
BA