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
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:
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
Oseltamivir
N8 structure used
Rudrawar et al, Nat Comm, 2011

8. 2012 Transmissible H5N1 Mutations
N158D
T318I, N224K
anitbody
Q226L
Newhouse et al, JACS 2009

9. New Class of HIV Drugs: Merck & Co.
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)
“ 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-0518
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
Opal App
MGLTools
CADD
Taverna
Vistrails
Kepler
Opal Application Services
Grid/Cloud Resources
CSF4/Globus
Condor
Fork
Condor pool
TeraGrid/PRAGMA Grid
PBS/SGE Clusters
Applications are first class services - users don’t have to specify paths to executables, working directories, etc
Examples of what the operations may look like
2. Security, state management, scheduling are all configured optionally
1. Jobs can even run on a Windows box - without a scheduler
3. Different services can exist in the same container - all accessible by separate URLs
4. Clients send command line arguments and input files to services (Base64 binary)

12. Virtualization for Bioscience Applications

13. Opal Plugins for Popular Workflow Software

14. Opal Web Service Client
OPAL NBCR
DUCKLING 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
Client Tool
TEXT MINING SYSTEM
Web Services (OPAL2)
NCBI data downloader
MetaMap
Network Generator
Sentence selector
Information element
recognizer
Visualizer
Data handler
Relation extractor
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
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 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: /2012/281078
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 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 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
Rocks and virtualization
gLite, globus
Data turbine
Duckling portal
Social networks?
Gfarm
Workflow systems
CSF4
Amazone EC2
Network?
TDW, SAGE
Opal 2, Opal OP