OFF-TARGET PIPELINE is a platform intended to carry out a recently introduced chemical systems biology approach for secondary target identification, but may also be useful to other applications in bioinformatics and drug discovery. Researchers can predict and compare protein functional sites, conduct structure-based docking, compute binding energy and compare electrostatic potential distribution within cavities. It also supports normalization of docking scores, information retrieval from PDB, and parsing of output files. All the afore-mentioned procedures are parallelized with significant speed gains and labor savings.
OFF-TARGET PIPELINE platform comprises:
PIPELINE currently supports local execution mode and dividing of work
load into individual threads running concurrently thus utilizing the CPU power to the maximum. It also supports massive submission
of APBS jobs to the respective
Opal-based Web-Server, in case no sufficient computer resources are available. Batch-mode execution on local computer clusters will be supported in the future versions (work
Evangelidis, T., Bourne, P.E., Xie, L., Xie, L.(2012) Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 PP. 32 - 39
Xie, L., Evangelidis, T., Xie, L., Bourne, P.E.
Drug discovery using chemical systems biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir(2011) PLoS Computational Biology 7 (4)
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