Linked Life Data

17510969

Source:http://linkedlifedata.com/resource/pubmed/id/17510969

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2007-7-26
pubmed:abstractText
Recognizing the structural similarity without significant sequence identity (called fold recognition) is the key for bridging the gap between the number of known protein sequences and the number of structures solved. Previously, we developed a fold-recognition method called SP(3) which combines sequence-derived sequence profiles, secondary-structure profiles and residue-depth dependent, structure-derived sequence profiles. The use of residue-depth-dependent profiles makes SP(3) one of the best automatic predictors in CASP 6. Because residue depth (RD) and solvent accessible surface area (solvent accessibility) are complementary in describing the exposure of a residue to solvent, we test whether or not incorporation of solvent-accessibility profiles into SP(3) could further increase the accuracy of fold recognition. The resulting method, called SP(4), was tested in SALIGN benchmark for alignment accuracy and Lindahl, LiveBench 8 and CASP7 blind prediction for fold recognition sensitivity and model-structure accuracy. For remote homologs, SP(4) is found to consistently improve over SP(3) in the accuracy of sequence alignment and predicted structural models as well as in the sensitivity of fold recognition. Our result suggests that RD and solvent accessibility can be used concurrently for improving the accuracy and sensitivity of fold recognition. The SP(4) server and its local usage package are available on http://sparks.informatics.iupui.edu/SP4.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1097-0134
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
68
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
636-45
pubmed:dateRevised
2007-12-3
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Fold recognition by concurrent use of solvent accessibility and residue depth.
pubmed:affiliation
Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural