PHOSIDA

Names
More detailed information about this field from each metasource.

PHOSIDA
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

phosida
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

Other names: phosida

Phosphorylation sites in various species identified by mass spectrometry

Webpage:

http://www.phosida.com

Publications:

Publications
More detailed information about this field from each metasource.

PHOSIDA 2011: the posttranslational modification database
PMID: 21081558
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

http://nar.oxfordjournals.org/content/39/suppl_1/D253
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

PHOSIDA 2011: the posttranslational modification database PubMed citations: 197.

197 articles citing: PHOSIDA 2011: the posttranslational modification database

Pumilio protects Xbp1 mRNA from regulated Ire1-dependent decay. PMID:35332141
Comprehensive identification of protein orthologs in the family Ascoviridae facilitates an understanding of phylogenomics, protein conservation, and phosphorylation. PMID:35246734
Biosynthesis and the Roles of Plant Sterols in Development and Stress Responses. PMID:35216448
KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. PMID:35011609
Clostridioides difficile Phosphoproteomics Shows an Expansion of Phosphorylated Proteins in Stationary Growth Phase. PMID:34986318
Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene. PMID:34970290
Phosphoproteomic Analysis Reveals Downstream PKA Effectors of AKAP Cypher/ZASP in the Pathogenesis of Dilated Cardiomyopathy. PMID:34966794
CRYPTOCHROMES promote daily protein homeostasis. PMID:34842284
CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. PMID:34681716
Kinase-Catalyzed Biotinylation to Map Cell Signaling Pathways: Application to Epidermal Growth Factor Signaling. PMID:34491762
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
HIM-17 regulates the position of recombination events and GSP-1/2 localization to establish short arm identity on bivalents in meiosis. PMID:33883277
Drosophila Homeodomain-Interacting Protein Kinase (Hipk) Phosphorylates the Hippo/Warts Signalling Effector Yorkie. PMID:33668437
Chronic caloric restriction maintains a youthful phosphoproteome in aged skeletal muscle. PMID:33529682
Post-Translational Modifications of G Protein-Coupled Receptors Control Cellular Signaling Dynamics in Space and Time. PMID:33268549
Local Myo9b RhoGAP activity regulates cell motility. PMID:33268376
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. PMID:33166149
STRIPAK regulates Slik localization to control mitotic morphogenesis and epithelial integrity. PMID:32960945
Phosphorylation by Aurora B kinase regulates caspase-2 activity and function. PMID:32811973
Regulation of histone deacetylase activities and functions by phosphorylation and its physiological relevance. PMID:32683534
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. PMID:32676006
Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. PMID:32648529
Role of Cyclin-Dependent Kinase 1 in Translational Regulation in the M-Phase. PMID:32605021
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans. PMID:32430394
Efficient manipulation and generation of Kirchhoff polynomials for the analysis of non-equilibrium biochemical reaction networks. PMID:32316881
Specificity in PDZ-peptide interaction networks: Computational analysis and review. PMID:32289118
Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. PMID:32245944
Molecular Basis of the Mechanisms Controlling MASTL. PMID:31852836
PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer. PMID:31399573
Large-scale Discovery of Substrates of the Human Kinome. PMID:31324866
An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships Between Kinase Activity and Phosphorylation. PMID:31227600
Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers. PMID:31152607
Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia 'He Xie'. PMID:31106836
The carboxy-terminus, a key regulator of protein function. PMID:31106589
Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. PMID:30986076
Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. PMID:30916345
KSIMC: Predicting Kinase⁻Substrate Interactions Based on Matrix Completion. PMID:30646505
The Atypical MAP Kinase ErkB Transmits Distinct Chemotactic Signals through a Core Signaling Module. PMID:30612939
Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. PMID:30577541
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. PMID:30397019
qPhos: a database of protein phosphorylation dynamics in humans. PMID:30380102
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Phosphoregulation of the intracellular termini of K+-Cl- cotransporter 2 (KCC2) enables flexible control of its activity. PMID:30201606
Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling. PMID:30108418
Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PMID:30096183
Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression. PMID:30009260
PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. PMID:29876573
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
HDAC Inhibition Improves the Sarcoendoplasmic Reticulum Ca2+-ATPase Activity in Cardiac Myocytes. PMID:29385061
High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing. PMID:29358376
Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. PMID:29344887
Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management. PMID:29204081
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells. PMID:29176673
Channel Nucleoporins Recruit PLK-1 to Nuclear Pore Complexes to Direct Nuclear Envelope Breakdown in C. elegans. PMID:29065307
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. PMID:29036382
Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy. PMID:28933595
Cip29 is phosphorylated following activation of the DNA damage response in Xenopus egg extracts. PMID:28715428
Phosphorylation-mediated Regulatory Networks in Mycelia of Pyricularia oryzae Revealed by Phosphoproteomic Analyses. PMID:28706003
A casein kinase 1 prevents expulsion of the oocyte meiotic spindle into a polar body by regulating cortical contractility. PMID:28701347
BERing the burden of damage: Pathway crosstalk and posttranslational modification of base excision repair proteins regulate DNA damage management. PMID:28629773
Designing disorder: Tales of the unexpected tails. PMID:28516025
Loss of Elp3 Impairs the Acetylation and Distribution of Connexin-43 in the Developing Cerebral Cortex. PMID:28507509
The physical characteristics of human proteins in different biological functions. PMID:28459865
Polo-like kinase-dependent phosphorylation of the synaptonemal complex protein SYP-4 regulates double-strand break formation through a negative feedback loop. PMID:28346135
Phosphorylation of zinc channel ZIP7 drives MAPK, PI3K and mTOR growth and proliferation signalling. PMID:28205653
The Link between Protein Kinase CK2 and Atypical Kinase Rio1. PMID:28178206
Anillin Phosphorylation Controls Timely Membrane Association and Successful Cytokinesis. PMID:28081137
Identification of SUMO modification sites in the base excision repair protein, Ntg1. PMID:27839712
Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias. PMID:27810942
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. PMID:27789692
Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction. PMID:27651752
Changes in cardiac Nav1.5 expression, function, and acetylation by pan-histone deacetylase inhibitors. PMID:27638876
Tale of a multifaceted co-activator, hADA3: from embryogenesis to cancer and beyond. PMID:27605378
Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family. PMID:27519537
Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages. PMID:27486199
Revealing disease-associated pathways by network integration of untargeted metabolomics. PMID:27479327
Proteomic discovery of host kinase signaling in bacterial infections. PMID:27440122
PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. PMID:27437197
Identification of Phosphorylated Cyclin-Dependent Kinase 1 Associated with Colorectal Cancer Survival Using Label-Free Quantitative Analyses. PMID:27383761
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PMID:27332813
Ligand stimulation of CD95 induces activation of Plk3 followed by phosphorylation of caspase-8. PMID:27325299
Phosphorylation acts positively and negatively to regulate MRTF-A subcellular localisation and activity. PMID:27304076
Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set. PMID:27183223
dbPAF: an integrative database of protein phosphorylation in animals and fungi. PMID:27010073
The Functional Significance of Posttranslational Modifications on Polo-Like Kinase 1 Revealed by Chemical Genetic Complementation. PMID:26919439
Evidence supporting a critical contribution of intrinsically disordered regions to the biochemical behavior of full-length human HP1γ. PMID:26680990
Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1. PMID:26669440
Discovery of a nucleocytoplasmic O-mannose glycoproteome in yeast. PMID:26644575
Comparative proteomic analysis of compartmentalised Ras signalling. PMID:26620772
Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level. PMID:26543102
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. PMID:26494363
Synaptic Effects of Munc18-1 Alternative Splicing in Excitatory Hippocampal Neurons. PMID:26407320
Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function. PMID:26344097
The Polycystin-1, Lipoxygenase, and α-Toxin Domain Regulates Polycystin-1 Trafficking. PMID:26311459
PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications. PMID:26283093
Proteomic Analysis Reveals Distinct Metabolic Differences Between Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) and Macrophage Colony Stimulating Factor (M-CSF) Grown Macrophages Derived from Murine Bone Marrow Cells. PMID:26229149
Mapping the SUMOylated landscape. PMID:26185901
Real-time and simultaneous monitoring of the phosphorylation and enhanced interaction of p53 and XPC acidic domains with the TFIIH p62 subunit. PMID:26029824
Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. PMID:25949811
Multidimensional proteomics for cell biology. PMID:25857810
dbPSP: a curated database for protein phosphorylation sites in prokaryotes. PMID:25841437
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Web resources for mass spectrometry-based proteomics. PMID:25721607
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
The acquisition of novel N-glycosylation sites in conserved proteins during human evolution. PMID:25628020
TXNDC5, a newly discovered disulfide isomerase with a key role in cell physiology and pathology. PMID:25526565
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. PMID:25514926
NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. PMID:25491371
Dynamic conformations of nucleophosmin (NPM1) at a key monomer-monomer interface affect oligomer stability and interactions with granzyme B. PMID:25490769
Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. PMID:25483092
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
Exploiting holistic approaches to model specificity in protein phosphorylation. PMID:25324856
Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. PMID:25093911
Interplay of DNA damage and cell cycle signaling at the level of human replication protein A. PMID:25091156
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. PMID:25042424
Identification of extracellular signal-regulated kinase 1 (ERK1) direct substrates using stable isotope labeled kinase assay-linked phosphoproteomics. PMID:25022875
The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. PMID:25018669
AMP-activated protein kinase phosphorylates EMCV, TMEV and SafV leader proteins at different sites. PMID:24999048
Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences. PMID:24963377
Mycobacterium tuberculosis supports protein tyrosine phosphorylation. PMID:24927537
Emerging mechanisms of mRNP remodeling regulation. PMID:24923990
Cardiac extracellular proteome profiling and membrane topology analysis using glycoproteomics. PMID:24920555
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
A novel regulatory locus of phosphorylation in the C terminus of the potassium chloride cotransporter KCC2 that interferes with N-ethylmaleimide or staurosporine-mediated activation. PMID:24849604
Transgenic tobacco overexpressing Brassica juncea HMG-CoA synthase 1 shows increased plant growth, pod size and seed yield. PMID:24847714
Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects. PMID:24833420
Classification of intrinsically disordered regions and proteins. PMID:24773235
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. PMID:24771658
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
Interactome analysis of AMP-activated protein kinase (AMPK)-α1 and -β1 in INS-1 pancreatic beta-cells by affinity purification-mass spectrometry. PMID:24625528
LAceP: lysine acetylation site prediction using logistic regression classifiers. PMID:24586884
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. PMID:24574112
An unbiased proteomic screen reveals caspase cleavage is positively and negatively regulated by substrate phosphorylation. PMID:24556848
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
CUL4A ubiquitin ligase: a promising drug target for cancer and other human diseases. PMID:24522884
Interleukin-1-induced changes in the glioblastoma secretome suggest its role in tumor progression. PMID:24503185
Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry. PMID:24495382
Deep proteome mapping of mouse kidney based on OFFGel prefractionation reveals remarkable protein post- translational modifications. PMID:24495006
Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PMID:24465218
Encephalomyocarditis virus leader is phosphorylated by CK2 and syk as a requirement for subsequent phosphorylation of cellular nucleoporins. PMID:24335301
Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow. PMID:24322422
A perspective on proteomics in cell biology. PMID:24284280
Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins. PMID:24260572
Effects of IL-6 on pyruvate dehydrogenase regulation in mouse skeletal muscle. PMID:24221357
Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism. PMID:24200585
Silencing of the tandem pore domain halothane-inhibited K+ channel 2 (THIK2) relies on combined intracellular retention and low intrinsic activity at the plasma membrane. PMID:24163367
RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. PMID:24040939
Circumventing embryonic lethality with Lcmt1 deficiency: generation of hypomorphic Lcmt1 mice with reduced protein phosphatase 2A methyltransferase expression and defects in insulin signaling. PMID:23840384
Odin (ANKS1A) modulates EGF receptor recycling and stability. PMID:23825523
Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. PMID:23807285
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
Characterizing the convergence of protein kinase CK2 and caspase-3 reveals isoform-specific phosphorylation of caspase-3 by CK2α': implications for pathological roles of CK2 in promoting cancer cell survival. PMID:23599180
Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output. PMID:23554854
Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes. PMID:23364837
Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. PMID:23360999
Phosphorylation at intrinsically disordered regions of PAM2 motif-containing proteins modulates their interactions with PABPC1 and influences mRNA fate. PMID:23340509
CELFish ways to modulate mRNA decay. PMID:23328451
Assembly of the SLIP1-SLBP complex on histone mRNA requires heterodimerization and sequential binding of SLBP followed by SLIP1. PMID:23286197
RNA-binding proteins as a point of convergence of the PI3K and p38 MAPK pathways. PMID:23272005
GTSE1 is a microtubule plus-end tracking protein that regulates EB1-dependent cell migration. PMID:23236459
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. PMID:23193284
A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis. PMID:23140645
Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus. PMID:23115289
Cell cycle regulation by the intrinsically disordered proteins p21 and p27. PMID:22988851
P(3)DB: An Integrated Database for Plant Protein Phosphorylation. PMID:22973285
The CDK9 tail determines the reaction pathway of positive transcription elongation factor b. PMID:22959624
The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination. PMID:22907757
Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. PMID:22899623
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Toward quantitative phosphotyrosine profiling in vivo. PMID:22677333
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. PMID:22669653
Leveraging proteomics to understand plant-microbe interactions. PMID:22645586
Phosphorylation of intrinsically disordered regions in remorin proteins. PMID:22639670
MMFPh: a maximal motif finder for phosphoproteomics datasets. PMID:22531218
Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT. PMID:22509746
The extracellular signal-regulated kinase 3 (mitogen-activated protein kinase 6 [MAPK6])-MAPK-activated protein kinase 5 signaling complex regulates septin function and dendrite morphology. PMID:22508986
The application of selective reaction monitoring confirms dysregulation of glycolysis in a preclinical model of schizophrenia. PMID:22420779
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. PMID:22373819
Modification site localization scoring: strategies and performance. PMID:22328712
Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. PMID:22307624
Chaperon-like Activation of Serum-Inducible Tryptophanyl-tRNA Synthetase Phosphorylation through Refolding as a Tool for Analysis of Clinical Samples. PMID:22191002
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. PMID:22135298
Phosphoproteomic studies of receptor tyrosine kinases: future perspectives. PMID:22134727
Activity regulation of adenosine deaminases acting on RNA (ADARs). PMID:22113393
Insights into phosphorylation-dependent mechanisms regulating USP1 protein stability during the cell cycle. PMID:22101265
Aminoacyl-tRNA synthetases and tumorigenesis: more than housekeeping. PMID:21941282
A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1. PMID:21851590
Regulation of caspase pathways by protein kinase CK2: identification of proteins with overlapping CK2 and caspase consensus motifs. PMID:21750976
Identification of kalirin-7 as a potential post-synaptic density signaling hub. PMID:21488700
On the cutting edge: post-translational modifications in cytokinesis. PMID:21349716
http://nar.oxfordjournals.org/content/39/suppl_1/D253

Tags:

Tags
More detailed information about this field from each metasource.

protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein modifications
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:51.239393

protein sequence protein sequence motifs and active sites protein modifications proteomics sequence sites, features and motifs proteins

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SuperSite

CoPS

ProTeus

Minimotif Miner

PDBSite

mutLBSgeneDB

SitEx

MeMotif

PhosphoSite Plus

Phospho3D

eF-site - Electrostatic surface of Functional site

SpliceAid

PROSITE

PreDREM

PRIDB

O-GLYCBASE

Integrated resource of protein families, domains and functional sites

FireDB

Major Intrinsic Proteins Modification Database

PRINTS