aiding computer aided drug design
DESCRIPTION
slides presented in USM IpharmTRANSCRIPT
![Page 1: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/1.jpg)
Aiding Computer Aided Drug Design
Mohd Shahir Shamsir (PhD)
Bioinformatics Research Group (BIRG)
Department of Biological Sciences,
Faculty of Bioscience & Bioengineering
Universiti Teknologi Malaysia
![Page 2: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/2.jpg)
Summary
• Aiding Computer Aided Drug Design
• Greasing the gears of CADD• Gaming gears• Video
![Page 3: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/3.jpg)
CADD is a specialised discipline that uses computational
methodsto simulate drug-receptor interactions – Richard
M casey
Computer aided drug design (CADD)
is a specialized discipline that uses computational methods to simulate drug-receptor interactions
Richard M. Casey
![Page 4: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/4.jpg)
CADD methods are heavily dependent on bioinformatics
tools, applications and databases.
CADD methods are heavily dependent on bioinformatics tools, applications and databases.
![Page 5: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/5.jpg)
CADD can metaphorically be an engine with many bioinformatics “gears” contributing towards the functioning of this “Engine”. Among these gears are homology modeling, similarity searchers, physicochemical modeling, virtual High
Throughput screening, drug lead optimization, drug bioavailability, drug bioactivity, sequence analysis. All of these is expected to translate into reduced time-to-market, cost savings and new insight into drug research.
Virtual High-Throughput Screening (vHTS)
Sequence Analysis
Homology Modeling Similarity Searches
Drug Lead Optimization
Physicochemical Modeling
Drug Bioavailability and Bioactivity
Cost Savings Time-to-Market
Insight
Computer Aided Drug Design
![Page 6: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/6.jpg)
Docking gears for example have varieties of tools that have
evolved
![Page 7: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/7.jpg)
We can aid/assist CADD by ‘greasing’
the ‘gears’ .Greasing CADD
![Page 8: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/8.jpg)
Interactions are key in ‘greasing’ the research gears. Science happens not just because of people doing experiments but because they are discussing those experiments
Christopher Surridge,Managing Editor PLoS ONE
Science happens not just because of people doing experiments but because they are discussing those experiments
![Page 9: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/9.jpg)
Greasing using Web 2.0 would enable easier collaboration between researchers and
research groups.Greasing using Web 2.0
![Page 10: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/10.jpg)
Multiple tools mostly user generated that has user generated content in mind
![Page 11: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/11.jpg)
Propels by a state of mind where users i.e. YOU generate content to be shared with other users
![Page 12: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/12.jpg)
Community and social collaboration
![Page 13: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/13.jpg)
Many examples of tools of web 2.0
![Page 14: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/14.jpg)
Tools created by the African Continent – unrestricted
creativity
![Page 15: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/15.jpg)
Landscape breakdown of how these tool are connected to
generate WEB 2.0
![Page 16: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/16.jpg)
Easier to Collaborate
• Collaborative tools examples
• Google Docs• Microsoft Office Live• Zoho• Thinkfree• Zimbra• springnote
![Page 17: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/17.jpg)
Yugma – a web conferencing tool - http://www.yugma.com/
![Page 18: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/18.jpg)
Freemind – a web based collaborative mind mapping tool
- http://freemind.sourceforge.net/
wiki/index.php/Main_Page
![Page 19: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/19.jpg)
Slideshare – to share slides for reseach presentations -
http://www.slideshare.net/
![Page 20: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/20.jpg)
Research computing is currently very fragmentedExisting approaches do not scale up to the amount of data now commonMany chemical informatics tools are obscure, difficult to use and access
Scientists’ questions are not that complex, but finding the answers is currently very time consuming and/or complex (for a human)“has anybody patented this chemical structure I just made?”
“can I get hold of a compound that might bind to the active site of this protein I just resolved?”“which compounds in this series are least likely to exhibit toxic effects?”
Answers are often “stale” after a short period of time – questions need to be re-answered as new information is generatedAlmost all available systems are passive, and follow the
(web) browsing modelThere tends to be one interface for every data source
(or encompassing just a few)
Scalability
passive
Scalability issue
Similarity Searches Research fragmentation
Complex questions
New pespective from new information
usability
Single interfaceaccessibility
Integrating CADD gears
![Page 21: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/21.jpg)
Automated Bioinformatics Workflows Tools
• Examples such as • Taverna - http://taverna.sourceforge.net/• Swami - http://www.ngbw.org/• Systems Biology Workbench - http://www.sys-bio.org/index.htm• SCSC Workbench - http://workbench.sdsc.edu/Integrating
CADD gears
![Page 22: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/22.jpg)
Amazon web services for easier biological data retrievalEasier data retrieval
![Page 23: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/23.jpg)
1. Annotated Human Genome Data provided by ENSEMBL (172GB).
2. GenBank provided by the National Center for Biotechnology Information (250GB)
3. UniGene provided by the National Center for Biotechnology Information (10 GB)
Easier data retrieval
![Page 24: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/24.jpg)
Digital Collaborations
![Page 25: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/25.jpg)
Initiated by O-Reilly meeting in 2004 called sci-foo
![Page 26: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/26.jpg)
Replicated in Second life (SL)
![Page 27: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/27.jpg)
Virtual meeting
![Page 28: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/28.jpg)
Virtual meeting
![Page 29: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/29.jpg)
Examples of material found on SL
![Page 30: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/30.jpg)
Gaming gears for CADD
Gaming Gears for CADD
![Page 31: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/31.jpg)
PS3?
![Page 32: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/32.jpg)
PS3!!
![Page 33: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/33.jpg)
First PS3 cluster for research by Dr Frank Mueller of North
Carolina University
![Page 34: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/34.jpg)
Warhawk Server Cluster
Costs lessReduced heatMinimum space
![Page 35: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/35.jpg)
CUDA support by n-VIDIA
![Page 36: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/36.jpg)
Statistics by Folding@Home
![Page 37: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/37.jpg)
Up and running eHITS application using PS3 by
SimBioSys Inc
![Page 38: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/38.jpg)
Video about Web 2.0VIDEO
![Page 39: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/39.jpg)
CADD still need hard working people.
CADD
![Page 40: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/40.jpg)
creditsImages from
![Page 41: Aiding Computer Aided Drug Design](https://reader036.vdocuments.net/reader036/viewer/2022081422/555db7ebd8b42a68328b5440/html5/thumbnails/41.jpg)
Questions