Biosciences Working Group Update

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/KukminGlyco-M*Grid NBCR CADD

3. Phylogenetic analysis based upon representative NA sequences and structures Human Swine origin Avian origin *structure available Li 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: Russell et al, Nature, 443: 45-49 (2006). Amaro et al, JACS, 2007

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

8. 2012 Transmissible H5N1 Mutations N158D Q226L Newhouse et al, JACS 2009

9. Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor Development Discovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock:Schames, … & McCammon, J. Med. Chem. (released on web, early 2004) MK-0518 “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). 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. Source: A. McCammon

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

11. Opal WS: Transparent Access Layer for Applications CADD Taverna Vistrails Kepler Opal App MGLTools Opal Application Services Grid/Cloud Resources CSF4/Globus Condor Fork PBS/SGE Clusters Condor pool TeraGrid/PRAGMA Grid

12. Virtualization for Bioscience Applications

13. Opal Plugins for Popular Workflow Software

14. http://opal-duckling.escience.cn http://ws.nbcr.net/opal2/dashboard OPAL Services @ NBCR DUCKLING Portal @ CNIC Output URL User Management Job Result Opal Web Service Client Web Service Application UIs Submit Job (Service URL) Metadata Cache Opal Service List Job History Application Metadata

15. InSilicoCell System architecture Web Services (OPAL2) Client Tool TEXT MINING SYSTEM NCBI datadownloader MetaMap Network Generator Information element recognizer Sentence selector Visualizer Relation extractor Data handler 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 • Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, Int J Comp Sci Issue, 2011, 8(5):180-183 Database Prototype of Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, http://herbaldb.farmasi.ui.ac.id 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 281078, 6 pages, doi:10.1155/2012/281078 • 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. 2011 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. PRAGMA 18, San Diego Nornisah Mohamed, USM

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

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