MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
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چکیده
منابع مشابه
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequ...
متن کامل3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures.
Many studies have used position-specific scoring matrices (PSSM) profiles to characterize residues in protein structures and to predict a broad range of protein features. Moreover, PSSM profiles of Protein Data Bank (PDB) entries have been recalculated in many works for different purposes. Although the computational cost of calculating a single PSSM profile is affordable, many statistical studi...
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A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the recent Crit...
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Protein sequence alignmentmay be viewed as either a classification or amultiple hypothesis testing problem.Whereas the type one error of a method is often studied for randomly generated sequences, the power is best investigated based on real protein sequences. The SCOP data base and its protein classification is used to investigate both the power and the type one error of sequence alignment as ...
متن کاملThe ProDom database of protein domain families
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail ([email protected]) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows ...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2006
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkj043