Journal ArticleDOI
pLogo: a probabilistic approach to visualizing sequence motifs
TLDR
The pLogo is described, a motif visualization in which residue heights are scaled relative to their statistical significance, in which real-time conditional probability calculations and visualizations are supported.Abstract:
Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.read more
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Journal ArticleDOI
Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center
James Marks,Krishna Kannan,Emily J. Roncase,Dorota Klepacki,Amira Kefi,Cédric Orelle,Nora Vazquez-Laslop,Alexander S. Mankin +7 more
TL;DR: It is shown that the activity of chloramphenicol and linezolid critically depends on the nature of specific amino acids of the nascent chain carried by the ribosome and by the identity of the residue entering the A site, which indicates that the nascent protein modulates the properties of the Ribosomal catalytic center and affects binding of its ligands.
Journal ArticleDOI
Casein kinase: the triple meaning of a misnomer.
TL;DR: A short historical explanation will be provided accounting for the usage of the same misnomer to denote three unrelated classes of protein kinases, together with an update of current knowledge of these pleiotropic enzymes, playing very distinct biological roles.
Journal ArticleDOI
Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).
TL;DR: A chemoenzymatic method is introduced for the site‐specific extraction of O‐linked glycopeptides (EXoO), which enabled the mapping of over 3,000 O‐ linked glycosylation sites and definition of their glycans on over 1,000 proteins in human kidney tissues, T cells, and serum.
Journal ArticleDOI
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Zhen Chen,Xuhan Liu,Fuyi Li,Chen Li,Chen Li,Tatiana T. Marquez-Lago,André Leier,Tatsuya Akutsu,Geoffrey I. Webb,Dakang Xu,Dakang Xu,Alexander Ian Smith,Lei Li,Kuo-Chen Chou,Jiangning Song +14 more
TL;DR: A novel computational framework, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs), is proposed, using deep, bidirectional, long short-term memory recurrent neural networks for accurate and systematic mapping of eight major types of lysin PTMs in the human and mouse proteomes.
Journal ArticleDOI
The human O-GlcNAcome database and meta-analysis.
Eugenia Wulff-Fuentes,Rex R. Berendt,Logan Massman,Laura Danner,Florian Malard,Jeet Vora,Robel Kahsay,Stephanie Olivier-Van Stichelen +7 more
TL;DR: In this article, an extensive inventory of human O-glcNAcylated proteins, their O-GlcNAc sites, identification methods, and corresponding references are provided.
References
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Journal ArticleDOI
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
Journal ArticleDOI
Sequence logos: a new way to display consensus sequences
Thomas D. Schneider,R M Stephens +1 more
TL;DR: From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content at every position in a site or sequence.
Journal ArticleDOI
A C-terminal signal prevents secretion of luminal ER proteins
Sean Munro,Hugh R.B. Pelham +1 more
TL;DR: It is proposed that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.
Journal ArticleDOI
The P-loop--a common motif in ATP- and GTP-binding proteins.
TL;DR: Current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.
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