03 Drug Design - d32ogoqmya1dw8.cloudfront.net€¦ · Drug design exemplar code A program structured like drug design soVware 1. Generate ligands to try for par4cular protein –

1

csinparallel.org

UsingParallelCompu4nginDrugDesign

RichardA.Brown,St.OlafElizabethShoop,MacalesterCollegeSuzanneJ.MaFhews,WestPointJoelC.Adams,CalvinCollege

2

csinparallel.org

Howdopharmaceu4calcompaniesdesignthemedicinesweuse?

3

csinparallel.org

Howmedicineswork

•  OurDNAislikeabookofrecipes

•  Insteadoffood,DNAcontainstheinstruc4onsformakingproteinsinourbodies

4

csinparallel.org

Howmedicineswork

•  Aprotein’sshapedeterminesthefunc4onitperformsinaperson’sbody

•  Todesignadrug,wecanfindligands(newpieces)tochangeaprotein’sshape

5

csinparallel.org

Howmedicineswork

6

csinparallel.org

StrategyfordrugdesignsoVware

1.   Generateligandstotryforpar4cularprotein–  Someligandswillfit,somewon’t

2.  Computeascoreforeachligandthatsimulateshowwellitwill:–  fitthatprotein;and–  produceadesiredshapechange

3.  Iden4fythehighestscoringligandsforactualsynthesis(produc4on)andtes4ng

7

csinparallel.org

DrugdesignexemplarcodeAprogramstructuredlikedrugdesignsoVware

1.   Generateligandstotryforpar4cularprotein–  Randomcharacterstringsofrandomlengths

2.  Computeascoreforeachligand–  Compareformaximummatch

withstringrepresen4ngaprotein–  Inser4onsanddele4onsallowed

3.  Iden4fythehighestscoringligands

8

csinparallel.org

AprogramstructuredlikedrugdesignsoVware1.   Generateligandstotryforpar4cularprotein–  Fast

2.  Computeascoreforeachligand–  Takesalong4me–  ParallelizebyusingmulAple

computaAonthreadsfordifferentligands

3.  Iden4fythehighestscoringligands–  Fast–justsortandfindmaximum

Drugdesignexemplarcode

9

csinparallel.org

DrugdesignexemplarcodeCommand-linearguments:

./drugdesign-sta4cthreadsmaxlencount •  threadsisnumberofsimultaneousthreads•  maxlenismaximumlengthofaligand– Eachligandhasrandomlengthuptothismax

•  countisnumberofligandstoscore