Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

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dc.catalogadoraba
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.contributor.authorMarti Renom, M. A.
dc.date.accessioned2025-02-06T19:57:47Z
dc.date.available2025-02-06T19:57:47Z
dc.date.issued2006
dc.description.abstractReduced or simplified amino acid alphabets group the 20 naturally occurring amino acids into a smaller number of representative protein residues. To date, several reduced amino acid alphabets have been proposed, which have been derived and optimized by a variety of methods. The resulting reduced amino acid alphabets have been applied to pattern recognition, generation of consensus sequences from multiple alignments, protein folding, and protein structure prediction. In this work, amino acid substitution matrices and statistical potentials were derived based on several reduced amino acid alphabets and their performance assessed in a large benchmark for the tasks of sequence alignment and fold assessment of protein structure models, using as a reference frame the standard alphabet of 20 amino acids. The results showed that a large reduction in the total number of residue types does not necessarily translate into a significant loss of discriminative power for sequence alignment and fold assessment. Therefore, some definitions of a few residue types are able to encode most of the relevant sequence/structure information that is present in the 20 standard amino acids. Based on these results, we suggest that the use of reduced amino acid alphabets may allow to increasing the accuracy of current substitution matrices and statistical potentials for the prediction of protein structure of remote homologs.
dc.format.extent10 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1002/prot.20881
dc.identifier.eissn1097-0134
dc.identifier.issn0887-3585
dc.identifier.urihttps://doi.org/10.1002/prot.20881
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102195
dc.identifier.wosidWOS:000237863100025
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.issue.numero4
dc.language.isoen
dc.nota.accesocontenido parcial
dc.pagina.final995
dc.pagina.inicio986
dc.revistaProteins
dc.rightsacceso restringido
dc.subjectStatistical potentials
dc.subjectSequence align-ment
dc.subjectFold recognition
dc.subjectReduced aminoacid alphabets
dc.subject.ddc570
dc.subject.deweyBiología
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleAccuracy of sequence alignment and fold assessment using reduced amino acid alphabets
dc.typeartículo
dc.volumen63
sipa.codpersvinculados82342
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