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PARALLEL ALGORITHM FOR DISCOVERING AND COMPARING THREE-DIMENSIONAL PROTEINS PATTERNS

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dc.creatorALEJANDRO MAURICIO VALDÉS JIMÉNEZ
dc.date2024
dc.date.accessioned2025-01-10T15:49:02Z
dc.date.available2025-01-10T15:49:02Z
dc.date.issued2024
dc.description.abstractIDENTIFYING CONSERVED (SIMILAR) THREE-DIMENSIONAL PATTERNS AMONG A SET OF PROTEINS CAN BE HELPFUL FOR THE RATIONAL DESIGN OF POLYPHARMACOLOGICAL DRUGS. SOME AVAILABLE TOOLS ALLOW THIS IDENTIFICATION FROM A LIMITED PERSPECTIVE, ONLY CONSIDERING THE AVAILABLE INFORMATION, SUCH AS KNOWN BINDING SITES OR PREVIOUSLY ANNOTATED STRUCTURAL MOTIFS. THUS, THESE APPROACHES DO NOT LOOK FOR SIMILARITIES AMONG ALL PUTATIVE ORTHOSTERIC AND OR ALLOSTERIC BINDINGS SITES BETWEEN PROTEIN STRUCTURES. TO OVERCOME THIS TECH-WEAKNESS GEOMFINDER WAS DEVELOPED, AN ALGORITHM FOR THE ESTIMATION OF SIMILARITIES BETWEEN ALL PAIRS OF THREE-DIMENSIONAL AMINO ACIDS PATTERNS DETECTED IN ANY TWO GIVEN PROTEIN STRUCTURES, WHICH WORKS WITHOUT INFORMATION ABOUT THEIR KNOWN PATTERNS. EVEN THOUGH GEOMFINDER IS A FUNCTIONAL ALTERNATIVE TO COMPARE SMALL STRUCTURAL PROTEINS, IT IS COMPUTATIONALLY UNFEASIBLE FOR THE CASE OF LARGE PROTEIN PROCESSING AND THE ALGORITHM NEEDS TO IMPROVE ITS PERFORMANCE. THIS WORK PRESENTS SEVERAL PARALLEL VERSIONS OF THE GEOMFINDER TO EXPLOIT SMPS, DISTRIBUTED MEMORY SYSTEMS, HYBRID VERSION OF SMP AND DISTRIBUTED MEMORY SYSTEMS, AND GPU BASED SYSTEMS. RESULTS SHOW SIGNIFICANT IMPROVEMENTS IN PERFORMANCE AS COMPARED TO THE ORIGINAL VERSION AND ACHIEVE UP TO 24.5X SPEEDUP WHEN ANALYZING PROTEINS OF AVERAGE SIZE AND UP TO 95.4X IN LARGER PROTEINS.
dc.formatapplication/pdf
dc.identifier.doi10.1109 /TCBB.2024. 3367789
dc.identifier.issn1557-9964
dc.identifier.issn1545-5963
dc.identifier.urihttps://repositorio.ubiobio.cl/handle/123456789/13787
dc.languagespa
dc.publisherIEEE-ACM Transactions on Computational Biology and Bioinformatics
dc.relation.uri10.1109 /TCBB.2024. 3367789
dc.rightsPUBLICADA
dc.subjectthree-dimensional patterns discovering
dc.subjectproteins
dc.subjectparallel and distributed programming
dc.subjectOpenMP
dc.subjectMPI
dc.subjectCUDA
dc.titlePARALLEL ALGORITHM FOR DISCOVERING AND COMPARING THREE-DIMENSIONAL PROTEINS PATTERNS
dc.typeARTÍCULO
dspace.entity.typePublication
ubb.EstadoPUBLICADA
ubb.Otra ReparticionDEPARTAMENTO DE SISTEMAS DE INFORMACION
ubb.SedeCONCEPCIÓN
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