Presentation on theme: "Biosciences Working Group Update"— Presentation transcript:
1 Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USAHabibah Wahab, Ph.D., USM, MalaysiaHosted by Monash UniversityMelbourne, Australia, Apr 17-19, 2012
2 Transparent access of applications on Avian Flu Grid through middleware CNIC Duckling PortalKonkuk/Kukmin Glyco-M*GridNBCR CADD
3 Phylogenetic analysis based upon representative NA sequences and structures HumanSwine originAvian origin*structure availableLi et al, Nat Struc Mol Biol, 2010
4 2009 N1 Crystal does not contain 150 cavity Li et al, Nat Struc Mol Biol, 2010
5 Group 1 and 2 neuraminidases 2 phylogenetically distinct groups:Recently a crystal structure for N1 (a group 1 NA) was released. This structure revealed a flexible loop and a new pocket adjacent to the active site that can potentially exploited for drug discovery against this enzyme.Russell et al, Nature, 443: (2006).Amaro et al, JACS, 2007
6 C-3 Derivatives of Zanamivir-like Compounds Lock 150 Cavity Open OseltamivirN8 structure usedRudrawar et al, Nat Comm, 2011
9 New Class of HIV Drugs: Merck & Co. Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor DevelopmentDiscovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock: Schames, … & McCammon, J. Med. Chem. (released on web, early 2004)“ Exploration of the structural basis for this unexpected result … suggests an approach to the development of integrase inhibitors with unique resistance profiles.”D. Hazuda et al., Proc. Natl. Acad. Sci. USA (Aug. 2004), refers to Schames, et al. (2004).MK-0518February, 2006 – Phase III Clinical TrialsFebruary, 2007 – Name announced:Isentress (raltegravir)October, 2007 – FDA “fast track” approvalNew Class of HIV Drugs: Merck & Co.Source: A. McCammon
11 Opal WS: Transparent Access Layer for Applications Opal AppMGLToolsCADDTavernaVistrailsKeplerOpal Application ServicesGrid/Cloud ResourcesCSF4/GlobusCondorForkCondor poolTeraGrid/PRAGMA GridPBS/SGE ClustersApplications are first class services - users don’t have to specify paths to executables, working directories, etcExamples of what the operations may look like2. Security, state management, scheduling are all configured optionally1. Jobs can even run on a Windows box - without a scheduler3. Different services can exist in the same container - all accessible by separate URLs4. Clients send command line arguments and input files to services (Base64 binary)
14 Opal Web Service Client OPAL NBCRDUCKLING CNICOutput URLUser ManagementJob ResultOpal Web Service ClientWeb ServiceApplication UIsSubmit Job (Service URL)Metadata CacheOpal Service ListJob HistoryApplication Metadata
15 InSilicoCell System architecture Client ToolTEXT MINING SYSTEMWeb Services (OPAL2)NCBI data downloaderMetaMapNetwork GeneratorSentence selectorInformation elementrecognizerVisualizerData handlerRelation extractorInformation handlerKISTI, Seok Jong Yu
17 University of Indonesia Progress Update Member (alphabethicaly ordered)Abdul Mun'im (Phytochemistry)Alhadi Bustamam (GPU Computing)Arry Yanuar (Pharmaceutical Chemistry)Heru Suhartanto (High Performance and Numerical Computing)
18 University of Indonesia Working Group DatabasePrototype of Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, http://herbaldb.farmasi.ui.ac.idMedicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, Int J Comp Sci Issue, 2011, 8(5):Member :Prof. Heru Suhartanto, Ph.D (High Performance and Numerical Computing)Dr. Arry Yanuar (Pharmaceutical Chemistry)Alhadi Bustamam, Ph.D. (GPU Computing)Dr. Abdul Mun'im (Phytochemistry)
19 University of Indonesia Working Group Recent Publication (ordered based on author in the previous slide)Berna Elya, Katrin Basah, Abdul Mun'im, Wulan Yuliastuti, Anastasia Bangun, and Eva Kurnia Septiana, Screening of 𝛼-Glucosidase Inhibitory Activity from Some Plants of Apocynaceae, Clusiaceae, Euphorbiaceae, and Rubiaceae, Journal of Biomedicine and Biotechnology, Volume 2012 (2012), Article ID , 6 pages, doi: /2012/281078Bustamam A, Burrage K, Hamilton NA., Fast Parallel Markov Clustering in Bioinformatics using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format. IEEE/ACM Trans Comput Biol Bioinform Mar 30.Hayun, Arry Yanuar, Muhammad Hanafi, and Sumi Hudiyono PWS, Virtual Screening of 2,3-Disubstituted-4(3H)-Quinazolinones Possessing Benzenesulfonamide Moiety for Selective COX-2 Inhibitor., Bioinformation. 2011; 7(5): 246–250Heru Suhartanto, Arry Yanuar , M.H. Hilman, Ari Wibisono and Toni Dermawan, Performance Analysis Cluster Computing Environment on Molecular Dynamics Simulation of RAD GTPase and LOX-Curcumin Molecule with AMBER, Int J Comp Sci Issue, 2012, Vol. No. 2 (in-press).
20 University of Indonesia Working Group On progress Research ActivitiesIn Silico Screening of Antimalarial Activity from Indonesian Medicinal Plants Database.In Silico Screening of HIV-1 Enzymes inhibitor Activity from Indonesian Medicinal Plants Database in GPU Environment.Alpha-glucosidase inhibition activity from Indonesian Medicinal PlantsDesign and synthesis of new COX-2 inhibitor.
21 2 – 4 March 2010PRAGMA 18, San DiegoNornisah Mohamed, USM
22 Hierarchical Map Reduce (HMR) Application:AutoDock Virtual ScreeningYuan Luo, IU
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