Download - Aiding Computer Aided Drug Design
Aiding Computer Aided Drug Design
Mohd Shahir Shamsir (PhD)
Bioinformatics Research Group (BIRG)
Department of Biological Sciences,
Faculty of Bioscience & Bioengineering
Universiti Teknologi Malaysia
Summary
• Aiding Computer Aided Drug Design
• Greasing the gears of CADD• Gaming gears• Video
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
CADD methods are heavily dependent on bioinformatics
tools, applications and databases.
CADD methods are heavily dependent on bioinformatics tools, applications and databases.
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
Docking gears for example have varieties of tools that have
evolved
We can aid/assist CADD by ‘greasing’
the ‘gears’ .Greasing CADD
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
Greasing using Web 2.0 would enable easier collaboration between researchers and
research groups.Greasing using Web 2.0
Multiple tools mostly user generated that has user generated content in mind
Propels by a state of mind where users i.e. YOU generate content to be shared with other users
Community and social collaboration
Many examples of tools of web 2.0
Tools created by the African Continent – unrestricted
creativity
Landscape breakdown of how these tool are connected to
generate WEB 2.0
Easier to Collaborate
• Collaborative tools examples
• Google Docs• Microsoft Office Live• Zoho• Thinkfree• Zimbra• springnote
Yugma – a web conferencing tool - http://www.yugma.com/
Freemind – a web based collaborative mind mapping tool
- http://freemind.sourceforge.net/
wiki/index.php/Main_Page
Slideshare – to share slides for reseach presentations -
http://www.slideshare.net/
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
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
Amazon web services for easier biological data retrievalEasier data retrieval
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
Digital Collaborations
Initiated by O-Reilly meeting in 2004 called sci-foo
Replicated in Second life (SL)
Virtual meeting
Virtual meeting
Examples of material found on SL
Gaming gears for CADD
Gaming Gears for CADD
PS3?
PS3!!
First PS3 cluster for research by Dr Frank Mueller of North
Carolina University
Warhawk Server Cluster
Costs lessReduced heatMinimum space
CUDA support by n-VIDIA
Statistics by Folding@Home
Up and running eHITS application using PS3 by
SimBioSys Inc
Video about Web 2.0VIDEO
CADD still need hard working people.
CADD
creditsImages from
Questions