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dc.contributor.author
Fuglebakk, Edvin
dc.contributor.author
Echave, Julian
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dc.contributor.author
Reuter, Nathalie
dc.date.available
2023-05-17T14:24:34Z
dc.date.issued
2012-10
dc.identifier.citation
Fuglebakk, Edvin; Echave, Julian; Reuter, Nathalie; Measuring and comparing structural fluctuation patterns in large protein datasets; Oxford University Press; Bioinformatics (Oxford, England); 28; 19; 10-2012; 2431-2440
dc.identifier.issn
1367-4803
dc.identifier.uri
http://hdl.handle.net/11336/197788
dc.description.abstract
Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of ex- perimental and theoretical work on protein dynamics. Further insight into the dynamics?function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native struc- ture. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. Results: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than struc- tural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evo- lutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Oxford University Press
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Protein Dynamics
dc.subject
Protein Classification
dc.subject
Protein Evolution
dc.subject.classification
Físico-Química, Ciencia de los Polímeros, Electroquímica
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dc.subject.classification
Ciencias Químicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
Measuring and comparing structural fluctuation patterns in large protein datasets
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2023-05-16T14:12:20Z
dc.journal.volume
28
dc.journal.number
19
dc.journal.pagination
2431-2440
dc.journal.pais
Reino Unido
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dc.journal.ciudad
Oxford
dc.description.fil
Fil: Fuglebakk, Edvin. University of Bergen; Noruega
dc.description.fil
Fil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Reuter, Nathalie. University of Bergen; Noruega
dc.journal.title
Bioinformatics (Oxford, England)
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformatics/article/28/19/2431/288157
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1093/bioinformatics/bts445
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