Fold assessment for comparative protein structure modeling

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dc.catalogadoraba
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.contributor.authorSali, A.
dc.date.accessioned2025-02-06T19:46:55Z
dc.date.available2025-02-06T19:46:55Z
dc.date.issued2007
dc.description.abstractAccurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences.
dc.fechaingreso.objetodigital2025-05-04
dc.format.extent15 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1110/ps.072895107
dc.identifier.eissn1469-896X
dc.identifier.issn0961-8368
dc.identifier.pubmedid17905832
dc.identifier.pubmedidPMC2211691
dc.identifier.urihttps://doi.org/10.1110/ps.072895107
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102192
dc.identifier.wosidWOS:000250444400010
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.issue.numeroNo. 11
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final2426
dc.pagina.inicio2412
dc.revistaProtein science : a publication of the Protein Society
dc.rightsacceso abierto
dc.subject.ddc570
dc.subject.deweyBiología
dc.titleFold assessment for comparative protein structure modeling
dc.typeartículo
dc.volumenVol. 16
sipa.codpersvinculados82342
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