Phospho.ELM: a database of phosphorylation sites—update 2011

The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42 574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.

[1]  S. Parasuraman,et al.  Protein data bank , 2012, Journal of pharmacology & pharmacotherapeutics.

[2]  George M Church,et al.  Collection and Motif-Based Prediction of Phosphorylation Sites in Human Viruses , 2010, Science Signaling.

[3]  Yu Xue,et al.  A summary of computational resources for protein phosphorylation. , 2010, Current protein & peptide science.

[4]  S. Feller,et al.  The dawn of a new era in cell signalling research , 2010, Cell Communication and Signaling.

[5]  Zhaohui S. Qin,et al.  A Global Protein Kinase and Phosphatase Interaction Network in Yeast , 2010, Science.

[6]  R. Linding,et al.  Simplistic pathways or complex networks? , 2010, Current opinion in genetics & development.

[7]  Mike Tyers,et al.  PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae , 2010, Database J. Biol. Databases Curation.

[8]  Jakub Pas,et al.  ELM: the status of the 2010 eukaryotic linear motif resource , 2009, Nucleic Acids Res..

[9]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[10]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2009 update , 2009, Nucleic Acids Res..

[11]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[12]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[13]  Leslie M Loew,et al.  Molecular machines or pleiomorphic ensembles: signaling complexes revisited , 2009, Journal of biology.

[14]  S. Lemeer,et al.  The phosphoproteomics data explosion. , 2009, Current opinion in chemical biology.

[15]  Toby J Gibson,et al.  Cell regulation: determined to signal discrete cooperation. , 2009, Trends in biochemical sciences.

[16]  Tony Pawson,et al.  Positive Selection of Tyrosine Loss in Metazoan Evolution , 2009, Science.

[17]  S. Gygi,et al.  Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution , 2009, Science.

[18]  Tony Pawson,et al.  Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases , 2009, Science Signaling.

[19]  Lila M. Gierasch,et al.  Sending Signals Dynamically , 2009, Science.

[20]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[21]  Ruedi Aebersold,et al.  PhosphoPep—a database of protein phosphorylation sites in model organisms , 2008, Nature Biotechnology.

[22]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[23]  S. Skvortsov,et al.  Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network , 2008, Proteomics.

[24]  Walter Kolch,et al.  Proteomics and phosphoproteomics for the mapping of cellular signalling networks , 2008, Proteomics.

[25]  Heribert Hirt,et al.  Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks , 2008, Proteomics.

[26]  Peer Bork,et al.  SMART 6: recent updates and new developments , 2008, Nucleic Acids Res..

[27]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[28]  Dong Xu,et al.  P3DB: a plant protein phosphorylation database , 2008, Nucleic Acids Res..

[29]  Jos Boekhorst,et al.  Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes , 2008, Genome Biology.

[30]  Adrian Whitty,et al.  Cooperativity and biological complexity. , 2008, Nature chemical biology.

[31]  G. Lienhard,et al.  Non-functional phosphorylations? , 2008, Trends in biochemical sciences.

[32]  Rodrigo Lopez,et al.  A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences , 2008, BMC Bioinformatics.

[33]  John R Yates,et al.  Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. , 2008, Journal of proteome research.

[34]  M. Mann,et al.  PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites , 2007, Genome Biology.

[35]  Tony Pawson,et al.  NetworKIN: a resource for exploring cellular phosphorylation networks , 2007, Nucleic Acids Res..

[36]  Allegra Via,et al.  Phospho.ELM: a database of phosphorylation sites—update 2008 , 2007, Nucleic Acids Res..

[37]  Yaoqi Zhou,et al.  Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties , 2007, Proteins.

[38]  P. Bork,et al.  Systematic Discovery of In Vivo Phosphorylation Networks , 2007, Cell.

[39]  H. Kitano.  A robustness-based approach to systems-oriented drug design , 2007, Nature Reviews Drug Discovery.

[40]  W. Lim,et al.  Docking interactions in protein kinase and phosphatase networks. , 2006, Current opinion in structural biology.

[41]  Allegra Via,et al.  Phospho3D: a database of three-dimensional structures of protein phosphorylation sites , 2006, Nucleic Acids Res..

[42]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[43]  Steven P Gygi,et al.  Phosphoproteomic Analysis of the Developing Mouse Brain*S , 2004, Molecular & Cellular Proteomics.

[44]  Steven P Gygi,et al.  Large-scale characterization of HeLa cell nuclear phosphoproteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[45]  J. Kornhauser,et al.  PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation , 2004, Proteomics.

[46]  L. Iakoucheva,et al.  The importance of intrinsic disorder for protein phosphorylation. , 2004, Nucleic acids research.

[47]  P. Hornbeck,et al.  Phosphoprotein Analysis Using Antibodies Broadly Reactive against Phosphorylated Motifs* , 2002, The Journal of Biological Chemistry.

[48]  Christopher J. Oldfield,et al.  Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions , 2002, Journal of Molecular Evolution.

[49]  Hanno Steen,et al.  Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. , 2002, Trends in biotechnology.

[50]  A M Lesk,et al.  Interior and surface of monomeric proteins. , 1987, Journal of molecular biology.

[51]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[52]  Allegra Via,et al.  From sequence to structural analysis in protein phosphorylation motifs. , 2011, Frontiers in bioscience.

[53]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[54]  T. Gibson,et al.  Phospho . ELM : A database of experimentally verified phosphorylation sites in eukaryotic proteins , 2004 .