KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

被引:24
|
作者
Lange, Joanna [1 ,2 ,3 ]
Wyrwicz, Lucjan S. [1 ,2 ]
Vriend, Gert [3 ]
机构
[1] M Sklodowska Curie Mem Canc Ctr, Lab Bioinformat & Biostat, Warsaw, Poland
[2] Inst Oncol, Warsaw, Poland
[3] CMBI Radboudumc, NL-6525 GA Nijmegen, Netherlands
关键词
ACCURATE PREDICTION; DATABASE; REGIONS; SEARCH;
D O I
10.1093/bioinformatics/btv663
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence-structure-function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins.
引用
收藏
页码:932 / 936
页数:5
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