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rdf:type |
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lifeskim:mentions |
umls-concept:C0444504,
umls-concept:C0522503,
umls-concept:C0524637,
umls-concept:C1514562,
umls-concept:C1705273,
umls-concept:C1705274,
umls-concept:C1705275,
umls-concept:C1880389,
umls-concept:C1883204,
umls-concept:C1883221,
umls-concept:C2827501
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pubmed:issue |
2
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pubmed:dateCreated |
2009-1-30
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pubmed:abstractText |
Protein domain prediction is often the preliminary step in both experimental and computational protein research. Here we present a new method to predict the domain boundaries of a multidomain protein from its amino acid sequence using a fuzzy mean operator. Using the nr-sequence database together with a reference protein set (RPS) containing known domain boundaries, the operator is used to assign a likelihood value for each residue of the query sequence as belonging to a domain boundary. This procedure robustly identifies contiguous boundary regions. For a dataset with a maximum sequence identity of 30%, the average domain prediction accuracy of our method is 97% for one domain proteins and 58% for multidomain proteins. The presented model is capable of using new sequence/structure information without re-parameterization after each RPS update. When tested on a current database using a four year old RPS and on a database that contains different domain definitions than those used to train the models, our method consistently yielded the same accuracy while two other published methods did not. A comparison with other domain prediction methods used in the CASP7 competition indicates that our method performs better than existing sequence-based methods.
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-10508779,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-10592239,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-11038331,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-11752314,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-11752315,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-11866536,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-11911892,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-12032088,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-12441380,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-12651735,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-1438297,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-14500873,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-14579342,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-14962932,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-15093838,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-15103630,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-15789433,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-15840834,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-15978619,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16187362,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16254179,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16267083,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16381859,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16844982,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16845079,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-16863650,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17109407,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17272837,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17356578,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17373854,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17430199,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17553833,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-17572080,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-18056079,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-18261994,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-18436442,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-18619468,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-4351801,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-7020376,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-7723011,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-8804826,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-9254694,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-9309224,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19056827-9868374
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:status |
MEDLINE
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pubmed:month |
Feb
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pubmed:issn |
1362-4962
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
37
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
452-62
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
|
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pubmed:year |
2009
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pubmed:articleTitle |
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator.
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pubmed:affiliation |
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. raj@bioanalysis.org
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pubmed:publicationType |
Journal Article,
Comparative Study,
Research Support, U.S. Gov't, Non-P.H.S.,
Evaluation Studies
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