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Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by Monash University Melbourne, Australia,

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Presentation on theme: "Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by Monash University Melbourne, Australia,"— Presentation transcript:

1 Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by Monash University Melbourne, Australia, Apr 17-19, 2012

2 Transparent access of applications on Avian Flu Grid through middleware CNIC Duckling Portal Konkuk/Kukmin Glyco-M*Grid NBCR CADD

3 Phylogenetic analysis based upon representative NA sequences and structures Li et al, Nat Struc Mol Biol, 2010 Human Swine origin Avian origin *structure available

4 2009 N1 Crystal does not contain 150 cavity Li et al, Nat Struc Mol Biol, 2010

5 Group 1 and 2 neuraminidases Russell et al, Nature, 443: (2006). 2 phylogenetically distinct groups: Amaro et al, JACS, 2007

6 C-3 Derivatives of Zanamivir-like Compounds Lock 150 Cavity Open Rudrawar et al, Nat Comm, 2011 ZanamivirOseltamivir N8 structure used

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8 2012 Transmissibl e H5N1 Mutations N158D Q226L Newhouse et al, JACS 2009

9 Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor Development 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). Discovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock: Schames, … & McCammon, J. Med. Chem. (released on web, early 2004) February, 2006 – Phase III Clinical Trials February, 2007 – Name announced: Isentress (raltegravir) October, 2007 – FDA fast track approval New Class of HIV Drugs: Merck & Co. MK-0518 Source: A. McCammon

10 Relaxed complex scheme Amaro, Baron, and McCammon, J. Comp. Aid. Mol. Des.. (2008) Amaro & Li, Curr. Top. Med. Chem. (2009) Amaro & Li, Methods in Mol Bio, (2012). Infectious Diseases: HIV Influenza Virus Dengue Virus Neglected Diseases: African Sleeping Sickness Neurological Disorders: Alzheimers Disease

11 Condor poolTeraGrid/PRAGMA Grid PBS/SGE Clusters CSF4/Globu s Opal Application Services Opal AppMGLTools Kepler Opal WS: Transparent Access Layer for Applications Grid/Cloud Resources CADDVistrailsTaverna Condor Fork

12 Virtualization for Bioscience Applications

13 Opal Plugins for Popular Workflow Software

14 OPAL NBCR DUCKLING CNIC User Management Opal Web Service Client Application Metadata Submit Job (Service URL) Output URL Metadata Cache Job History Application UIs Opal Service List Job Result Web Service

15 TEXT MINING SYSTEM InSilicoCell System architecture Sentence selector Relation extractor Information element recognizer Data handler MetaMap Client Tool NCBI data downloader Network Generator Visualizer Information handler KISTI, Seok Jong Yu

16 BioKnowledge Viewer GUI

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 Database o Prototype of Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, Medicinal 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 -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/ Bustamam 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): 246–250 Heru 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 Activities In 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 Plants Design and synthesis of new COX-2 inhibitor.

21 2 – 4 March 2010 PRAGMA 18, San Diego21 Nornisah Mohamed, USM

22 Hierarchical Map Reduce (HMR) Yuan Luo, IU Application: AutoDock Virtual Screening

23 Karma Provenance System and Applications

24 Benchmarks Technology adopted and improved, Biosciences WG – Duckling portal – Gfarm – CSF4 – Network? – TDW, SAGE – Opal 2, Opal OP – Rocks and virtualization – gLite, globus – Data turbine – Social networks? – Workflow systems – Amazone EC2


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