03 drug design - d32ogoqmya1dw8.cloudfront.net€¦ · drug design exemplar code a program...
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csinparallel.org
UsingParallelCompu4nginDrugDesign
RichardA.Brown,St.OlafElizabethShoop,MacalesterCollegeSuzanneJ.MaFhews,WestPointJoelC.Adams,CalvinCollege
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Howdopharmaceu4calcompaniesdesignthemedicinesweuse?
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Howmedicineswork
• OurDNAislikeabookofrecipes
• Insteadoffood,DNAcontainstheinstruc4onsformakingproteinsinourbodies
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Howmedicineswork
• Aprotein’sshapedeterminesthefunc4onitperformsinaperson’sbody
• Todesignadrug,wecanfindligands(newpieces)tochangeaprotein’sshape
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Howmedicineswork
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StrategyfordrugdesignsoVware
1. Generateligandstotryforpar4cularprotein– Someligandswillfit,somewon’t
2. Computeascoreforeachligandthatsimulateshowwellitwill:– fitthatprotein;and– produceadesiredshapechange
3. Iden4fythehighestscoringligandsforactualsynthesis(produc4on)andtes4ng
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DrugdesignexemplarcodeAprogramstructuredlikedrugdesignsoVware
1. Generateligandstotryforpar4cularprotein– Randomcharacterstringsofrandomlengths
2. Computeascoreforeachligand– Compareformaximummatch
withstringrepresen4ngaprotein– Inser4onsanddele4onsallowed
3. Iden4fythehighestscoringligands
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AprogramstructuredlikedrugdesignsoVware1. Generateligandstotryforpar4cularprotein– Fast
2. Computeascoreforeachligand– Takesalong4me– ParallelizebyusingmulAple
computaAonthreadsfordifferentligands
3. Iden4fythehighestscoringligands– Fast–justsortandfindmaximum
Drugdesignexemplarcode
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DrugdesignexemplarcodeCommand-linearguments:
./drugdesign-sta4cthreadsmaxlencount • threadsisnumberofsimultaneousthreads• maxlenismaximumlengthofaligand– Eachligandhasrandomlengthuptothismax
• countisnumberofligandstoscore