Protein Sequence Threading: Averaging over Structures

Protein Sequence Threading: Averaging over Structures (2002)

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by Anthony J. Russell , Andrew E. Torda

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BibTeX

@MISC{Russell02proteinsequence,
    author = {Anthony J. Russell and Andrew E. Torda},
    title = {Protein Sequence Threading: Averaging over Structures},
    year = {2002}
}

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Abstract

Multiplesequencealignmentsare aroutinetoolinproteinfoldrecognition,butmultiplestructurealignmentsarecomputationallyless cooperative.Thisworkdescribesamethodforproteinsequencethreadingandsequence -to-structure alignmentsthatusesmultiplealignedstructures, theaimbeingtoimprovemodelsfromprotein threadingcalculations.Sequencesarealignedinto afieldduetocorrespondingsitesinhomologous proteins.Onthebasisofatestsetofmorethan570 proteinpairs,theproceduredoesimprovealignmentquality, althoughnomorethanaveragingover sequences.Fortheforcefieldtested,thebenefitof structureaveragingissmallerthanthatofadding sequencesimilaritytermsoracontributionfrom secondarystructurepredictions.Althoughthereis asignificantimprovementinthequalityofsequenceto -structurealignments,thisdoesnotdirectlytranslatetoanimmediateimprovementinfoldrecogni - tioncapability.Proteins2002;47:496--505.

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