ArticleBioinformatics (Oxford, England)2016
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Protein language model identifies disordered, conserved motifs implicated in phase separation.eLife · 2025Article
- Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins.The journal of physical chemistry. B · 2025Article
- SpatPPI: a geometric deep learning model for predicting protein-protein interactions involving intrinsically disordered regions.Genome biology · 2025Article
- Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.Cell · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- Untangling Zebrafish Genetic Annotation: Addressing Complexities and Nomenclature Issues in Orthologous Evaluation of TCOF1 and NOLC1.Journal of molecular evolution · 2024Article
- Assessing the role of evolutionary information for enhancing protein language model embeddings.Scientific reports · 2024Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.bioRxiv : the preprint server for biology · 2024Article
- Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2023Article
- Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions.PLoS computational biology · 2023Article
- The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.PloS one · 2023Article
- Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.Annual review of biophysics · 2022Review
- SETH predicts nuances of residue disorder from protein embeddings.Frontiers in bioinformatics · 2022Article
- Intrachain interaction topology can identify functionally similar intrinsically disordered proteins.Biophysical journal · 2021Article
- AJournal of medical genetics · 2020Article
- Article
- Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2019Article
- Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins.Scientific reports · 2019Article
- Conservation of Prion-Like Composition and Sequence in Prion-Formers and Prion-Like Proteins ofFrontiers in molecular biosciences · 2019Article
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3 authors.
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Abstract
unlabelledIntrinsically 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.
resultsMSAs 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. AVAILABILITY AND IMPLEMENTATION: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/ A standalone version is freely available. CONTACT: vriend@cmbi.ru.nl.
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