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

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, whic...

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Bibliographic Details
Published in:	Bioinformatics 2016-03, Vol.32 (6), p.932-936
Main Authors:	Lange, Joanna, Wyrwicz, Lucjan S, Vriend, Gert
Format:	Article
Language:	eng
Subjects:	Accessibility Alignment Applications Notes Bioinformatics Computer programs Intrinsically Disordered Proteins Knowledge base Knowledge Bases Proteins Sequence Alignment Servers (computers) Software
Online Access:	Get full text
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Summary:	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. 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. KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/ A standalone version is freely available. vriend@cmbi.ru.nl.
ISSN:	1367-4803 1367-4811 1460-2059