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