Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Journal of Proteome Research

• Publication date

  2004-02-28

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/PR0341033PMID 15253423
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Protein Kinase A Signaling Pathway Regulates Transcriptional Activity of SAF-1 by Unmasking Its DNA-binding Domains*

  2003cited by this paper
• Proteomic analysis of post-translational modifications

  2003cited by this paper
• Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome.

  2002cited by this paper
• Phosphoprotein Analysis Using Antibodies Broadly Reactive against Phosphorylated Motifs*

  2002cited by this paper
• A Mass Spectrometry-based Proteomic Approach for Identification of Serine/Threonine-phosphorylated Proteins by Enrichment with Phospho-specific Antibodies

  2002cited by this paper
• Structural basis and prediction of substrate specificity in protein serine/threonine kinases

  2002cited by this paper
• Protein kinase substrate recognition studied using the recombinant catalytic domain of AMP-activated protein kinase and a model substrate.

  2002cited by this paper
• Necdin is required for terminal differentiation and survival of primary dorsal root ganglion neurons.

  2002cited by this paper
• The origins of protein phosphorylation

  2002cited by this paper
• Phosphopeptide detection and sequencing by matrix-assisted laser desorption/ionization quadrupole time-of-flight tandem mass spectrometry.

  2002cited by this paper
• Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

  2002cited by this paper
• The existence of two distinct Wee1 isoforms in Xenopus: implications for the developmental regulation of the cell cycle

  2002cited by this paper
• PKB/Akt: a key mediator of cell proliferation, survival and insulin responses?

  2001cited by this paper
• Mass spectrometry in proteomics.

  2001cited by this paper
• Mass spectrometry allows direct identification of proteins in large genomes

  2001cited by this paper
• Phosphorylation of murine double minute clone 2 (MDM2) protein at serine-267 by protein kinase CK2 in vitro and in cultured cells.

  2001cited by this paper
• A motif-based profile scanning approach for genome-wide prediction of signaling pathways

  2001cited by this paper
• Phospho‐proteomics: Evaluation of the use of enzymatic de‐phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis

  2001cited by this paper
• Fate of Midbrain Dopaminergic Neurons Controlled by the Engrailed Genes

  2001cited by this paper
• Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors.

  2000cited by this paper
• Protein kinase-A dependent phosphorylation of transcription enhancer factor-1 represses its DNA-binding activity but enhances its gene activation ability.

  2000cited by this paper
• A Functionally Essential Domain of RFX5 Mediates Activation of Major Histocompatibility Complex Class II Promoters by Promoting Cooperative Binding between RFX and NF-Y

  2000cited by this paper
• Signaling—2000 and Beyond

  2000cited by this paper
• Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry.

  1999cited by this paper
• PhosphoBase, a database of phosphorylation sites: release 2.0

  1999cited by this paper
• Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.

  1999cited by this paper
• Identification of Regulatory Phosphorylation Sites in Mitogen-activated Protein Kinase (MAPK)-activated Protein Kinase-1a/p90 rsk That Are Inducible by MAPK*

  1998cited by this paper
• The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease.

  1998cited by this paper
• Protein kinase A-dependent phosphorylation modulates DNA-binding activity of hepatocyte nuclear factor 4

  1997cited by this paper
• The PROSITE database, its status in 1997

  1997cited by this paper
• Artificial Neural Networks for Molecular Sequence Analysis

  1997cited by this paper
• How do protein kinases recognize their substrates?

  1996cited by this paper
• Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

  1996cited by this paper
• Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks

  1996cited by this paper
• Phosphorylation of the Drosophila engrailed protein at a site outside its homeodomain enhances DNA binding

  1995cited by this paper
• The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1

  1995cited by this paper
• Use of an oriented peptide library to determine the optimal substrates of protein kinases.

  1994cited by this paper
• Structural framework for the protein kinase family.

  1992cited by this paper
• The regulation of transcription by phosphorylation.

  1992cited by this paper
• Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase.

  1991cited by this paper
• Proposal for a common nomenclature for sequence ions in mass spectra of peptides.

  1984cited by this paper
• Optimal spatial requirements for the location of basic residues in peptide substrates for the cyclic AMP-dependent protein kinase.

  1980cited by this paper

• InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics

  2025cites this paper
• Kinase-substrate prediction using an autoregressive model

  2025cites this paper
• Sulfur-Free Reversible Addition Fragmentation Chain Transfer Emulsion Polymerization Strategy for Electrochemical Analysis of Protein Kinase A Activity

  2024cites this paper
• CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov–Arnold network

  2024cites this paper
• Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites

  2022cites this paper
• Computational systems approach towards phosphoproteomics and their downstream regulation

  2022cites this paper
• A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction

  2022cites this paper
• Utilization of Landscape of Kinases and Phosphosites To Predict Kinase-Substrate Association

  2022cites this paper
• A Brief Review of Machine Learning Techniques for Protein Phosphorylation Sites Prediction

  2021cites this paper
• Special Issue on “New Advances in Cyclic AMP Signalling”—An Editorial Overview

  2020cites this paper
• In Silico Tools and Phosphoproteomic Software Exclusives

  2019influential citation
• Application of Machine Learning Techniques to Predict Protein Phosphorylation Sites

  2019cites this paper
• Prediction of phosphorylation sites based on granular support vector machine

  2019cites this paper
• Phosphorylation of TIP3 Aquaporins during Phaseolus vulgaris Embryo Development

  2019cites this paper
• iPhoPred: A Predictor for Identifying Phosphorylation Sites in Human Protein

  2019cites this paper
• Application of Proteomics Technologies in Oil Palm Research

  2018cites this paper
• A generic deep convolutional neural network framework for prediction of receptor–ligand interactions—NetPhosPan: application to kinase phosphorylation prediction

  2018cites this paper
• CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis

  2018cites this paper
• Toxoplasma gondii Requires Glycogen Phosphorylase for Balancing Amylopectin Storage and for Efficient Production of Brain Cysts

  2017influential citation
• Prediction of phosphorylation sites based on Krawtchouk image moments

  2017cites this paper
• PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

  2017cites this paper
• The cyclic AMP phosphodiesterase 4D5 (PDE4D5)/receptor for activated C-kinase 1 (RACK1) signalling complex as a sensor of the extracellular nano-environment.

  2017cites this paper
• Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells

  2016cites this paper
• Molecular interaction motifs in a system-wide network context: Computationally charting transient kinase-substrate phosphorylation events

  2016cites this paper
• Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

  2016cites this paper
• Critical Role of Cx40 in Reduced Endothelial Electrical Coupling by Lipopolysaccharide and Hypoxia-Reoxygenation

  2016cites this paper
• Caracterização de sítios conformacionais de fosforilação em proteínas

  2016cites this paper
• Exploring the Sequence Context of Phosphorylatable Amino Acids: The Contribution of the Upgraded MAPRes Tool

  2015cites this paper
• Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data

  2015cites this paper
• Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

  2015cites this paper
• A reverse-engineering approach to dissect post-translational modulators of transcription factor’s activity from transcriptional data

  2015cites this paper
• PhospredRF: Prediction of protein phosphorylation sites using a consensus of random forest classifiers

  2015cites this paper
• A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles.

  2015cites this paper
• Computational phosphorylation network reconstruction: methods and resources.

  2015cites this paper
• Proteomic profiling of fatty acid biosynthetic enzymes from oil palm chromoplast

  2015cites this paper
• JUPred_MLP: Prediction of Phosphorylation Sites Using a Consensus of MLP Classifiers

  2015cites this paper
• Protein folding creates structure-based, noncontiguous consensus phosphorylation motifs recognized by kinases

  2014cites this paper
• Data construction for phosphorylation site prediction

  2014cites this paper
• Toward a systems-level view of dynamic phosphorylation networks

  2014cites this paper
• Experimental and Computational Tools for Analysis of Signaling Networks in Primary Cells

  2014cites this paper
• Computational methods and opportunities for phosphorylation network medicine.

  2014cites this paper
• Phosphoproteomic Analysis of Protein Phosphorylation Networks in Tetrahymena thermophila, a Model Single-celled Organism.

  2014cites this paper
• Design and data analysis of kinome microarrays

  2014cites this paper
• PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

  2014influential citation
• Missense Variants of Uncertain Significance (VUS) Altering the Phosphorylation Patterns of BRCA1 and BRCA2

  2013cites this paper
• Phosphoproteomic Analysis of Protein Phosphorylation Networks in Tetrahymena thermophila, a Model Single-celled Organism*

  2013cites this paper
• Post-translational modifications and mass spectrometry detection.

  2013cites this paper
• Meta-prediction of phosphorylation sites with multiplicative weighted update algorithms

  2012cites this paper
• The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism

  2012cites this paper
• Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note

  2012cites this paper
• AMS 4.0: consensus prediction of post-translational modifications in protein sequences

  2012cites this paper
• An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells.

  2012cites this paper
• Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors.

  2012cites this paper
• Mass spectrometry in systems biology an introduction.

  2011cites this paper
• Computational prediction of eukaryotic phosphorylation sites

  2011cites this paper
• Graphlet Kernels for Prediction of Functional Residues in Protein Structures

  2010cites this paper
• Machine Learning Approaches to Bioinformatics

  2010cites this paper
• AMS 3.0: prediction of post-translational modifications

  2010cites this paper
• Nucleic Acids Research

  2010cites this paper
• Experimental and computational tools useful for (re)construction of dynamic kinase–substrate networks

  2009cites this paper
• NetPhosBac – A predictor for Ser/Thr phosphorylation sites in bacterial proteins

  2009cites this paper
• Data Mining for Phospho-Proteomics

  2009cites this paper
• Peptide microarrays for detailed, high-throughput substrate identification, kinetic characterization, and inhibition studies on protein kinase A.

  2009cites this paper
• Kinase-specific prediction of protein phosphorylation sites.

  2009cites this paper
• Identification of novel in vitro protein kinase A phosphorylation sites on recombinant non-muscle myosin light chain kinase: Nano-liquid chromatography tandem mass spectrometry methodology

  2008cites this paper
• Identification of phosphorylation sites of TOPORS and a role for phosphorylated residues in the regulation of ubiquitin and SUMO E3 ligase activity

  2008cites this paper
• Identification of Phosphorylation Sites Using SVMs

  2008cites this paper
• SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles

  2008cites this paper
• Protein Interaction Network Based Prediction of Domain-Domain and Domain-Peptide Interactions

  2008cites this paper
• Adaptive Locality-Effective Kernel Machine for protein phosphorylation site prediction

  2008cites this paper
• Distinction between human cytochrome P450 (CYP) isoforms and identification of new phosphorylation sites by mass spectrometry.

  2008cites this paper
• Ubiquitination is involved in glucose-mediated downregulation of GIP receptors in islets.

  2007cites this paper
• Predicting Protein Phosphorylation Sites with Neuralgenetic Network Algorithm

  2007cites this paper
• NetworKIN: a resource for exploring cellular phosphorylation networks

  2007cites this paper
• How to comprehensively analyse proteins and how this influences nutritional research

  2007cites this paper
• Identifying Atg1 Substrates: Four Means to an End

  2007cites this paper
• GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network.

  2007cites this paper
• Protein phosphorylation analysis by site-specific arginine-mimic labeling in gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

  2007cites this paper
• Systematic discovery of in vivo phosphorylation networks.

  2007influential citation
• Interpreting the protein language using proteomics

  2006cites this paper
• Phosphoproteomics toolbox: Computational biology, protein chemistry and mass spectrometry

  2006cites this paper
• Substrate specificity of protein kinases and computational prediction of substrates.

  2005cites this paper
• Association of Biomolecular Resource Facilities 2005 meeting. Biomolecular technologies: discovery to hypothesis

  2005cites this paper
• Chapter 5 Phosphorylation-specific analysis strategies for mass spectrometry: enhanced detection of phosphorylated proteins and peptides

  2005cites this paper
• Posttranslational modification of proteins

  2005cites this paper
• Incorporating hidden Markov models for identifying protein kinase‐specific phosphorylation sites

  2005cites this paper
• KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites

  2005cites this paper
• Fickle factor foils fat fate

  2005cites this paper
• Current Awareness on Comparative and Functional Genomics

  2004cites this paper
• Current literature in mass spectrometry

  2004cites this paper