biosciences working group update wilfred w. li, ph.d., ucsd, usa habibah wahab, ph.d., usm, malaysia...
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Biosciences Working Group Update
Wilfred W. Li, Ph.D., UCSD, USA
Habibah Wahab, Ph.D., USM, Malaysia
Hosted by Monash UniversityMelbourne, Australia, Apr 17-19, 2012
Transparent access of applications on Avian Flu Grid through middleware
CNIC Duckling Portal
Konkuk/KukminGlyco-M*Grid
NBCR CADD
Phylogenetic analysis based upon representative NA sequences and structures
Li et al, Nat Struc Mol Biol, 2010
HumanSwine originAvian origin
*structure available
2009 N1 Crystal does not contain 150 cavity
Li et al, Nat Struc Mol Biol, 2010
Group 1 and 2 neuraminidases
Russell et al, Nature, 443: 45-49 (2006).
2 phylogenetically distinct groups:
Amaro et al, JACS, 2007
C-3 Derivatives of Zanamivir-like Compounds Lock 150 Cavity Open
Rudrawar et al, Nat Comm, 2011
Zanamivir Oseltamivir
N8 structure used
2012 Transmissib
le H5N1 Mutations
N158D
Q226LNewhouse et al, JACS 2009
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 TrialsFebruary, 2007 – Name announced: Isentress (raltegravir)October, 2007 – FDA “fast track” approval
New Class of HIV Drugs: Merck & Co.
MK-0518
Source: A. McCammon
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: HIVInfluenza VirusDengue Virus
Neglected Diseases: African Sleeping Sickness
Neurological Disorders:Alzheimer’s Disease
Condor pool TeraGrid/PRAGMA Grid PBS/SGE Clusters
CSF4/Globus
Opal Application Services
Opal App MGLTools KeplerOpal WS: Transparent Access Layer for Applications
Grid/Cloud ResourcesGrid/Cloud Resources
CADD VistrailsTaverna
Condor Fork
Virtualization for Bioscience Applications
Opal Plugins for Popular Workflow Software
OPAL Services @ NBCROPAL Services @ NBCR DUCKLING Portal @ CNICDUCKLING Portal @ CNIC
User Management
Opal Web Service Client
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
http://opal-duckling.escience.cn
http://ws.nbcr.net/opal2/dashboard
TEXT MINING SYSTEM
InSilicoCell System architecture
Sentence selectorSentence selector
Relation extractorRelation extractor
Information elementInformation elementrecognizerrecognizer
Data handlerData handler
MetaMapMetaMap
Client Tool
NCBI dataNCBI datadownloaderdownloader
Network Network GeneratorGenerator
VisualizerVisualizer
Information Information handlerhandler
KISTI, Seok Jong Yu
BioKnowledge Viewer GUI
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)
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, http://herbaldb.farmasi.ui.ac.id
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
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)
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, 𝛼Clusiaceae, 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).
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.
2 – 4 March 2010 PRAGMA 18, San Diego 21
Hierarchical Map Reduce (HMR)
Yuan Luo, IU
Application: AutoDock Virtual Screening
Karma Provenance System and Applications
Benchmarks