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» SCOP: a Structural Classification of Proteins database
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BMCBI
2010
113views more  BMCBI 2010»
13 years 7 months ago
Efficient protein alignment algorithm for protein search
Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore ...
Zaixin Lu, Zhiyu Zhao, Bin Fu
BMCBI
2008
114views more  BMCBI 2008»
13 years 7 months ago
Combining classifiers for improved classification of proteins from sequence or structure
Background: Predicting a protein's structural or functional class from its amino acid sequence or structure is a fundamental problem in computational biology. Recently, there...
Iain Melvin, Jason Weston, Christina S. Leslie, Wi...
NAR
2007
90views more  NAR 2007»
13 years 7 months ago
The SUPERFAMILY database in 2007: families and functions
The SUPERFAMILY database provides protein domain assignments, at the SCOP ‘superfamily’ level, for the predicted protein sequences in over 400 completed genomes. A superfamily...
Derek Wilson, Martin Madera, Christine Vogel, Cyru...
BMCBI
2006
104views more  BMCBI 2006»
13 years 7 months ago
MANET: tracing evolution of protein architecture in metabolic networks
Background: Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionar...
Hee Shin Kim, Jay E. Mittenthal, Gustavo Caetano-A...
BIBE
2005
IEEE
126views Bioinformatics» more  BIBE 2005»
14 years 1 months ago
Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches
PSI-BLAST remains one of the popular tools for searching remote homologs in sequence databases. We recently demonstrated that hybrid alignment can function as the alignment core f...
Yuheng Li, Mario Lauria, Ralf Bundschuh