Avian Flu Grid http://avianflugrid.pragma-grid.net International Collaborative Environment for Team Science on Avian Influenza Thu, 29 May 2008 20:35:01 +0000 http://wordpress.org/?v=2.5.1 en Education http://avianflugrid.pragma-grid.net/news/education/ http://avianflugrid.pragma-grid.net/news/education/#comments Thu, 29 May 2008 20:31:38 +0000 admin http://avianflugrid.nbcr.net/?p=21 NBCR Summer Institute
PRAGMA Institute

]]> http://avianflugrid.pragma-grid.net/news/education/feed/ Methodology http://avianflugrid.pragma-grid.net/about/methodology/methodology/ http://avianflugrid.pragma-grid.net/about/methodology/methodology/#comments Thu, 29 May 2008 20:28:20 +0000 admin http://avianflugrid.nbcr.net/?p=20 Relaxed Complex Method

 

NAMD
Amber
Gromos
Gromacs

 

Virtual Screening

AutoDock
MGLTools

Resources

 

The RC/MD workflow is complex and computationally demanding, but with strong potentials for application to other infectious diseases. While the MD simulations are more scalable in a high performance computing cluster with low latency network, the virtual screening process requires little interprocessor communication and is highly suitable for a distributed grid environment. The Avian Flu Grid is an integrative effort based on the technology developed by several member institutes to support advanced scientific research for avian flu.
The calculations based on these state-of-the-art computational approaches is managed by the CSF4 meta-scheduler (http://gcsf.sourceforge.net) through either a portal environment (https://portal.pragma-grid.net:9443) or Opal-based application specific web services (http://nbcr.net/serivces) which leverages CSF4 for job distribution.
Long running MD simulations with a large number of processors are done using TeraGrid (http://www.teragrid.org) resources, and HPC resources available at the National Biomedical Computation Resource (http://nbcr.net), and Maui High Performance Computing Center (http://www.mhpcc.edu). The complex work flows are captured using the Vision workflow management tools (http://mgltools.scripps.edu).

 

Data
Computational data management and sharing across different sites is simplified using Gfarm (http://datafarm.apgrid.org). The simulation setup, and post-analysis are carried out using M*Grid and Glyco-M*Grid (http://www.mgrid.or.kr/), and virtual screening results are managed using the Scientific Data Grid (http://pragma.sdg.ac.cn/).
In addition, Glyco-M*Grid, a grid portal-based integrated environment for e-Glycomics, provides a powerful tool for tackling the glycobiology in the avian flu systems. Preliminary equilibration and minimization steps of the MD simulations as well as virtual screening experiments are carried using PRAGMA grid. Natural compound library is screened using the NaPIMM portal (http://www.usm.my).

]]> http://avianflugrid.pragma-grid.net/about/methodology/methodology/feed/ Specific Aims http://avianflugrid.pragma-grid.net/about/specific-aims/specific-aims/ http://avianflugrid.pragma-grid.net/about/specific-aims/specific-aims/#comments Thu, 29 May 2008 20:26:29 +0000 admin http://avianflugrid.nbcr.net/?p=19 The avian influenza virus type A, especially subtype H5N1, is becoming the world’s largest pandemic threat due to its high virulence and lethality rate in birds, quickly expanding host reservoir, and high rate of mutations. The two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA) of influenza virus play important roles in the interactions with cellular receptors containing terminal N-acetylneuraminic acid (Neu5Ac, or NANA) moieties, aka, sialic acids. The approved anti-influenza drugs, oseltamivir and zanamivir, inhibit H5N1 infection by targeting the NA active site, thereby blocking the release of newly formed viral particles. However, research has shown that antigenic drift may give rise to new strains that are resistant to existing NA inhibitors and antigenic shift could give rise to new virulent subtypes of the flu virus.
Thus, it is crucial to design novel HA- and NA-targeted inhibitors, which can be used in combination for optimal prophylaxis and treatment. The Relaxed Complex (RC) scheme and Molecular Dynamics (MD) simulations have been applied on the two target proteins to capture key protein dynamics information and accounting for receptor flexibility. Research is under way to take advantage of novel loop flexibilities and changing cavity shapes adjacent to NA active site to discover novel NA inhibitors that may work in a way similar to the HIV integrase inhibitor, raltegravir, inspired by the RC/MD simulation procedures. Further investigation involves statistical cluster analysis for rational selection of representative HA/NA protein structure snapshots, which are used in the virtual screening with synthetic and natural compound libraries. Finally, the binding energies of the high scoring hits are re-scored using Molecular Mechanics-Poisson Bolzmann Surface Area (MM-PBSA) method before experimental validation and subsequent lead optimization.

]]> http://avianflugrid.pragma-grid.net/about/specific-aims/specific-aims/feed/ Computation Resources http://avianflugrid.pragma-grid.net/resources/computation/computation-resources/ http://avianflugrid.pragma-grid.net/resources/computation/computation-resources/#comments Thu, 29 May 2008 20:25:01 +0000 admin http://avianflugrid.nbcr.net/?p=18 NBCR
PRAGMA Grid
TeraGrid
Maui High Performance Computing Center
MGrid

]]> http://avianflugrid.pragma-grid.net/resources/computation/computation-resources/feed/ wiki http://avianflugrid.pragma-grid.net/resources/wiki/ http://avianflugrid.pragma-grid.net/resources/wiki/#comments Thu, 29 May 2008 20:19:35 +0000 admin http://avianflugrid.nbcr.net/?p=17 Project Wiki

]]> http://avianflugrid.pragma-grid.net/resources/wiki/feed/ Program Officers http://avianflugrid.pragma-grid.net/people/program-officers/program-officers/ http://avianflugrid.pragma-grid.net/people/program-officers/program-officers/#comments Thu, 29 May 2008 20:15:19 +0000 admin http://avianflugrid.nbcr.net/?p=16 Anne Westbrook, Ph.D.

Amber Stanley

and previously

Mary Kratz, Ph.D.

]]> http://avianflugrid.pragma-grid.net/people/program-officers/program-officers/feed/ Institutions http://avianflugrid.pragma-grid.net/people/institutions/institutions/ http://avianflugrid.pragma-grid.net/people/institutions/institutions/#comments Thu, 29 May 2008 20:13:28 +0000 admin http://avianflugrid.nbcr.net/?p=15 PRAGMA
NBCR
PRIME
University of Hawaii
Jilin University
AIST
University of Tsukuba
CNIC
Konkuk University
USM
NTU

]]> http://avianflugrid.pragma-grid.net/people/institutions/institutions/feed/ Portals http://avianflugrid.pragma-grid.net/resources/portals/ http://avianflugrid.pragma-grid.net/resources/portals/#comments Thu, 29 May 2008 20:10:33 +0000 admin http://avianflugrid.nbcr.net/?p=14 Avian Flu Grid Home Page
PRAGMA Biosciences Portal
Avian Flu Info (Chinese/English)
CNIC portal for Bird Flu and related Pandemic Diseases (Chinese)
Glyco-MGrid

]]> http://avianflugrid.pragma-grid.net/resources/portals/feed/ Web Sites http://avianflugrid.pragma-grid.net/related/web-sites/ http://avianflugrid.pragma-grid.net/related/web-sites/#comments Thu, 29 May 2008 20:09:26 +0000 admin http://avianflugrid.nbcr.net/?p=13 Options for the Control of Influenza VI
Avianflu.gov
CDC Influenza site
WHO Avian Flu site
Nature Magazine: Avian Flu Web Focus
Wikipedia on Bird Flu
Flu Wiki

]]> http://avianflugrid.pragma-grid.net/related/web-sites/feed/ Conferences and Workshops http://avianflugrid.pragma-grid.net/related/conferences/conferences-and-workshops/ http://avianflugrid.pragma-grid.net/related/conferences/conferences-and-workshops/#comments Thu, 29 May 2008 20:08:35 +0000 admin http://avianflugrid.nbcr.net/?p=12 Anti-influenza conference, June 2007
Options for Control of Influenza VI, June 2007
Bangkok International Conference on Avian Flu January 2008
World Summit on Antivirals, July 2008
BirdFlu September 2008

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