کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10869953 | 1073980 | 2015 | 9 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
TAPO: A combined method for the identification of tandem repeats in protein structures
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موضوعات مرتبط
علوم زیستی و بیوفناوری
علوم کشاورزی و بیولوژیک
دانش گیاه شناسی
پیش نمایش صفحه اول مقاله

چکیده انگلیسی
In recent years, there has been an emergence of new 3D structures of proteins containing tandem repeats (TRs), as a result of improved expression and crystallization strategies. Databases focused on structure classifications (PDB, SCOP, CATH) do not provide an easy solution for selection of these structures from PDB. Several approaches have been developed, but no best approach exists to identify the whole range of 3D TRs. Here we describe the TAndem PrOtein detector (TAPO) that uses periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational alphabets, residue contact maps, and arrangements of vectors of secondary structure elements. The benchmarking shows the superior performance of TAPO over the existing programs. In accordance with our analysis of PDB using TAPO, 19% of proteins contain 3D TRs. This analysis allowed us to identify new families of 3D TRs, suggesting that TAPO can be used to regularly update the collection and classification of existing repetitive structures.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: FEBS Letters - Volume 589, Issue 19, Part A, 14 September 2015, Pages 2611-2619
Journal: FEBS Letters - Volume 589, Issue 19, Part A, 14 September 2015, Pages 2611-2619
نویسندگان
Phuong Do Viet, Daniel B. Roche, Andrey V. Kajava,