PRAGMA Avian Flu Grid: Drug Discovery against Infectious Diseases Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia.

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Presentation transcript:

PRAGMA Avian Flu Grid: Drug Discovery against Infectious Diseases Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia

Accumulative Statistics on H5N1 March 19, 2008

Transparent access of applications on Avian Flu Grid through middleware Opal poster, PRAGMA 13 AFG poster, PRAGMA 13

Opal CSF4 Integration

Software Status from SCMSWeb

Vision Based Grid Workflow Environment Clementi et al, IEEE eScience 2008

Data visualization _____________________________________________________________ ___________________ | | | | | Clus | Lowest | Run | Mean | Num | Histogram -ter | Binding | | Binding | in | Rank | Energy | | Energy | Clus| _____|___________|_____|___________|_____|____:____|____:____|___ _:____|____:___ 1 | | 10 | | 6 |###### 2 | | 5 | | 4 |#### 3 | | 59 | | 6 |###### 4 | | 6 | | 10 |########## 5 | | 87 | | 4 |#### 6 | | 83 | | 9 |######### 7 | | 61 | | 4 |#### 8 | | 19 | | 1 |# 9 | | 9 | | 2 |## 10 | | 32 | | 20 |#################### 11 | | 95 | | 1 |# 12 | | 93 | | 1 |# 13 | | 27 | | 16 |################ 14 | | 75 | | 1 |# 15 | | 16 | | 4 |#### 16 | | 34 | | 1 |# 17 | | 77 | | 1 |# 18 | | 49 | | 2 |## 19 | | 11 | | 1 |# 20 | | 74 | | 3 |### 21 | | 41 | | 1 |# 22 | | 56 | | 1 |# 23 | | 90 | | 1 |# process

Glyco-Mgrid and VS-Mgrid Youngjin Choi, Karpjoo Jeong

Glycobiology of Neuraminidase Sharing of simulation data Sharing of knowledge and expertise CrystalMD-CHARMMMD-NAMD Youngjin Choi

NA active site domain is intrinsically flexible and offers new drug design opportunities

Top Hits

Drug Design and Discovery for Developing Countries, 3-5th July, 2008 Compound nameNumber of conformation Final Free energy, kcal/molInhibition constant, Ki MSC E-09 MSC E-09 MSC E-09 MSC E-10 MSC E-10 Top 5 compounds screened from MD trajectories of neuraminidase MSC986 MSC1026 MSC 1685 MSC 1880MSC 1941

Visualization of HA-Glycan Interactions Xu, et al. JMB, 2008 (submitted).

Session 1 Summary Hoon Choi, KISTI – E-Science Environment for Avian Flu PRAGMA 16 – bioinformatics session on flu data integration, epidemiologically Data sharing, flu sequence data with China, and other AP countries Thanh Truong, U Utah – CSE-online, 2 nd generation, Avisto – astonis.com, free for high school, supported by advertisement – Molecular design, workflow management, connecting different graphically represented modules – Privately funded development

More … Jincheol Kim, KISTI – DrugScreener-G, Eclipse platform, currently only supports gLite middleware. A platform to support different applications. – Motuer workflow engine for EGEE; Kepler ? – Support interoperation of gLite, UNICORE. – Will integrate Opal to DrugScreener-G, utilize Gfarm services for data sharing. Hongwen Yang, CNIC – Virtual screening database Lucy Liu – Qinghai Lake Avian Epidemiological Observerations – Joint Research Center for wild life studies – E-Science demo application E-science is a process, not the ultimate goal.

From here to PRAGMA 16 Proposed activities towards PRAGMA 16 – Large scale SNP analysis – KISTI, J. Kim – Avian Flu workshop – Expanded targets among other infectious diseases – Collaboration with EGEE drug discovery activities