Linked Life Data

17369627

Source:http://linkedlifedata.com/resource/pubmed/id/17369627

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2007-3-19
pubmed:abstractText
Root mean square deviation (RMSD) is often used to measure the difference between structures. We show mathematically that, for multiple structure alignment, the minimum RMSD (weighted at aligned positions or unweighted) for all pairs is the same as the RMSD to the average of the structures. Thus, using RMSD implies that the average is a consensus structure. We use this property to validate and improve algorithms for multiple structure alignment. In particular, we establish the properties of the average structure, and show that an iterative algorithm proposed by Sutcliffe and co-authors can find it efficiently--each iteration takes linear time and the number of iterations is small. We explore the residuals after alignment and assign weights to positions to identify aligned cores of structures. Observing this property also calls into question whether global RMSD is the right way to compare multiple protein structures, and guides the search for more local techniques.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1752-7791
pubmed:author
pubmed:issnType
Print
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
79-87
pubmed:dateRevised
2007-12-3
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Multiple structure alignment by optimal RMSD implies that the average structure is a consensus.
pubmed:affiliation
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3175, USA. xwang@cs.unc.edu
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural