title: KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.
abstract: 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.
authors.affiliation: Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and.
authors.forename: Joanna
authors.initials: J
authors.lastname: Lange
authors.affiliation: Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and.
authors.forename: Lucjan S
authors.initials: LS
authors.lastname: Wyrwicz
authors.affiliation: CMBI Radboudumc, 6525 GA, Nijmegen, The Netherlands.
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
mesh_terms: D064267:Intrinsically Disordered Proteins; D051188:Knowledge Bases; D011506:Proteins; D016415:Sequence Alignment; D012984:Software
chemical_list: D064267:Intrinsically Disordered Proteins; D011506:Proteins