Statistical potentials for fold assessment

Simple item page
dc.catalogadoraba
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.contributor.authorSánchez, R.
dc.contributor.authorSali, A.
dc.date.accessioned2025-02-06T19:56:54Z
dc.date.available2025-02-06T19:56:54Z
dc.date.issued2002
dc.description.abstractA protein structure model generally needs to be evaluated to assess whether or not it has the correct fold. To improve fold assessment, four types of a residue-level statistical potential were optimized, including distance-dependent, contact, ϕ/Ψ dihedral angle, and accessible surface statistical potentials. Approximately 10,000 test models with the correct and incorrect folds were built by automated comparative modeling of protein sequences of known structure. The criterion used to discriminate between the correct and incorrect models was the Z-score of the model energy. The performance of a Z-score was determined as a function of many variables in the derivation and use of the corresponding statistical potential. The performance was measured by the fractions of the correctly and incorrectly assessed test models. The most discriminating combination of any one of the four tested potentials is the sum of the normalized distance-dependent and accessible surface potentials. The distance-dependent potential that is optimal for assessing models of all sizes uses both Cα and Cβ atoms as interaction centers, distinguishes between all 20 standard residue types, has the distance range of 30 Å, and is derived and used by taking into account the sequence separation of the interacting atom pairs. The terms for the sequentially local interactions are significantly less informative than those for the sequentially nonlocal interactions. The accessible surface potential that is optimal for assessing models of all sizes uses Cβ atoms as interaction centers and distinguishes between all 20 standard residue types. The performance of the tested statistical potentials is not likely to improve significantly with an increase in the number of known protein structures used in their derivation. The parameters of fold assessment whose optimal values vary significantly with model size include the size of the known protein structures used to derive the potential and the distance range of the accessible surface potential. Fold assessment by statistical potentials is most difficult for the very small models. This difficulty presents a challenge to fold assessment in large-scale comparative modeling, which produces many small and incomplete models. The results described in this study provide a basis for an optimal use of statistical potentials in fold assessment.
dc.fechaingreso.objetodigital2025-05-04
dc.format.extent19 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1002/pro.110430
dc.identifier.eissn1469-896X
dc.identifier.issn0961-8368
dc.identifier.pubmedid11790853
dc.identifier.pubmedidPMC2373452
dc.identifier.urihttps://doi.org/10.1002/pro.110430
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102194
dc.identifier.wosidWOS:000173352700026
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.issue.numeroNo. 2
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final448
dc.pagina.inicio430
dc.revistaProtein science : a publication of the Protein Society
dc.rightsacceso abierto
dc.subjectModel evaluation
dc.subjectComparative modeling
dc.subjectFold assignment
dc.subjectFold assessment
dc.subjectStatistical poten-tials
dc.subjectLarge scale protein structure modeling
dc.subject.ddc570
dc.subject.deweyBiología
dc.titleStatistical potentials for fold assessment
dc.typeartículo
dc.volumenVol. 11
sipa.codpersvinculados82342
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Statistical potentials for fold assessment.pdf
Size:
470.34 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Artículos de revistas