Shapes of cell signaling

Cell signaling is a complex process organized in time and space. Signal transduction is constantly modulated by cell-intrinsic and cell-extrinsic input cues and the resulting phenotypic responses such as morphological can feed back into the system. This provides cells with a responsive, accurate, and rugged system to deal with changes in the surroundings or the genome. Whilst signaling networks (dynamic transient protein–protein interactions modulated by post-translational modifications in response to input cues) have been researched for decades, further analysis of their spatial organization is critical for both basic and disease biology and will benefit from recent advances in computational modeling and image analysis using deep/machine learning and in microscopy and imaging. Furthermore, mathematical modeling with reaction-diffusion approaches on time-varying geometries complements the investigations, allowing to conceptualize the organizational principles of signaling and information transduction in the four dimensions of time and space.Peer Reviewe

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

Phospho.ELM:a database of experimentally verified phosphorylation sites in eukaryotic proteins

BACKGROUND: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DESCRIPTION: Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.CONCLUSION: Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.</p