Phospho.ELM

Names
More detailed information about this field from each metasource.

Phospho.ELM
metasource: Fairsharing.org
version: None

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:30.253678

phospho.elm
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:30.253678

Other names: phospho.elm

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets.

Webpage:

http://phospho.elm.eu.org/index.html

Licence:

Name: Phospho.ELM Disclaimer
URL: http://phospho.elm.eu.org/disclaimer.html

Publications:

Publications
More detailed information about this field from each metasource.

Phospho.ELM: a database of phosphorylation sites--update 2011
PMID: 21062810
metasource: Fairsharing.org
version: None

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:30.253678

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
PMID: 15212693
metasource: Fairsharing.org
version: None

Phospho.ELM: a database of phosphorylation sites--update 2008
PMID: 17962309
metasource: Fairsharing.org
version: None

Phospho.ELM: a database of phosphorylation sites--update 2011 PubMed citations: 261.

261 articles citing: Phospho.ELM: a database of phosphorylation sites--update 2011

Mini-review: Recent advances in post-translational modification site prediction based on deep learning. PMID:35860402
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. PMID:35805150
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. PMID:35579274
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. PMID:35532924
TransPhos: A Deep-Learning Model for General Phosphorylation Site Prediction Based on Transformer-Encoder Architecture. PMID:35457080
Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer. PMID:35397555
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
A Transfer-Learning-Based Deep Convolutional Neural Network for Predicting Leukemia-Related Phosphorylation Sites from Protein Primary Sequences. PMID:35163663
EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning. PMID:35157015
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. PMID:34989786
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. PMID:34652972
Adipocytes disrupt the translational programme of acute lymphoblastic leukaemia to favour tumour survival and persistence. PMID:34535653
FSL-Kla: A few-shot learning-based multi-feature hybrid system for lactylation site prediction. PMID:34471495
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Phosphoproteomics Analysis Reveals a Pivotal Mechanism Related to Amino Acid Signals in Goat Fetal Fibroblast. PMID:34414225
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
DTL-DephosSite: Deep Transfer Learning Based Approach to Predict Dephosphorylation Sites. PMID:34249915
Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). PMID:34238254
Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs. PMID:34186244
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:34108016
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation. PMID:33846320
ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). PMID:33834021
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. PMID:33562780
KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. PMID:33556051
My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. PMID:33514395
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Mutational survivorship bias: The case of PNKP. PMID:33332469
Accurate prediction of kinase-substrate networks using knowledge graphs. PMID:33270624
The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture. PMID:33264611
PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification. PMID:33240890
DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands. PMID:33216893
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome. PMID:32900925
A SNP-mediated lncRNA (LOC146880) and microRNA (miR-539-5p) interaction and its potential impact on the NSCLC risk. PMID:32795333
KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins. PMID:32753030
Exploring protein phosphorylation by combining computational approaches and biochemical methods. PMID:32728408
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
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
Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. PMID:32547896
From Beef to Bees: High-Throughput Kinome Analysis to Understand Host Responses of Livestock Species to Infectious Diseases and Industry-Associated Stress. PMID:32499776
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PMID:32497121
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains. PMID:32443803
Genotype-phenotype analysis of LMNA-related diseases predicts phenotype-selective alterations in lamin phosphorylation. PMID:32413188
An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles. PMID:32397800
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1). PMID:32350110
Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. PMID:32245944
Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation. PMID:32203512
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
Molecular Basis of the Mechanisms Controlling MASTL. PMID:31852836
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. PMID:31848261
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
Substrate-based kinase activity inference identifies MK2 as driver of colitis. PMID:31617572
Resources to Discover and Use Short Linear Motifs in Viral Proteins. PMID:31427097
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Why do eukaryotic proteins contain more intrinsically disordered regions? PMID:31329574
Large-scale Discovery of Substrates of the Human Kinome. PMID:31324866
Evolution of protein kinase substrate recognition at the active site. PMID:31233486
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability. PMID:31196969
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. PMID:31161204
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
KSIMC: Predicting Kinase⁻Substrate Interactions Based on Matrix Completion. PMID:30646505
MoMo: discovery of statistically significant post-translational modification motifs. PMID:30596994
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. PMID:30577541
Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. PMID:30478315
Coupling function of cyclin-dependent kinase 2 and Septin2 in the promotion of hepatocellular carcinoma. PMID:30444001
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
AWESOME: a database of SNPs that affect protein post-translational modifications. PMID:30215764
Proteome-wide analysis of phospho-regulated PDZ domain interactions. PMID:30126976
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. PMID:30053270
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Reversible, functional amyloids: towards an understanding of their regulation in yeast and humans. PMID:29963943
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. PMID:29947803
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. PMID:29844483
Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. PMID:29344887
ksrMKL: a novel method for identification of kinase-substrate relationships using multiple kernel learning. PMID:29340231
A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships. PMID:29312990
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. PMID:29191787
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
Prediction of protein disorder based on IUPred. PMID:29076577
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. PMID:29036382
Systems-level identification of PKA-dependent signaling in epithelial cells. PMID:28973931
Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy. PMID:28933595
Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate. PMID:28837810
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory. PMID:28650961
Protein post-translational modifications: In silico prediction tools and molecular modeling. PMID:28458782
Methods, Tools and Current Perspectives in Proteogenomics. PMID:28456751
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. PMID:28387819
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Benchmarking substrate-based kinase activity inference using phosphoproteomic data. PMID:28200105
Interrogating the hidden phosphoproteome. PMID:28165663
Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines. PMID:28150249
iPTMnet: Integrative Bioinformatics for Studying PTM Networks. PMID:28150246
Protein Bioinformatics Databases and Resources. PMID:28150231
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. PMID:27939638
An atlas of human kinase regulation. PMID:27909043
Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. PMID:27852923
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells. PMID:27526785
Proteomic discovery of host kinase signaling in bacterial infections. PMID:27440122
PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. PMID:27437197
KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily. PMID:27357839
Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development. PMID:27150584
KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. PMID:27145998
HIPPO-Integrin-linked Kinase Cross-Talk Controls Self-Sustaining Proliferation and Survival in Pulmonary Hypertension. PMID:27119551
The end of a monolith: Deconstructing the Cnn-Polo interaction. PMID:27096551
Prioritizing functional phosphorylation sites based on multiple feature integration. PMID:27090940
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. PMID:27085803
Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. PMID:27067626
RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest. PMID:27066500
Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites. PMID:27046079
CCProf: exploring conformational change profile of proteins. PMID:27016699
The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. PMID:26960075
CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription. PMID:26942677
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
A Two-Immunoglobulin-Domain Transmembrane Protein Mediates an Epidermal-Neuronal Interaction to Maintain Synapse Density. PMID:26777275
Peptide Arrays for Kinome Analysis of Livestock Species. PMID:26664912
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation. PMID:26601103
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks. PMID:26572964
Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PMID:26509276
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
Kinase Identification with Supervised Laplacian Regularized Least Squares. PMID:26448296
An Amino-Terminal Polo Kinase Interaction Motif Acts in the Regulation of Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila. PMID:26447129
Recent findings and technological advances in phosphoproteomics for cells and tissues. PMID:26400465
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. PMID:26395771
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. PMID:26357075
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PMID:26312481
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
Study of phosphorylation events for cancer diagnoses and treatment. PMID:26055493
Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. PMID:25949811
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. PMID:25948583
A grammar inference approach for predicting kinase specific phosphorylation sites. PMID:25886273
Computational prediction of protein-protein interactions. PMID:25859943
dbPSP: a curated database for protein phosphorylation sites in prokaryotes. PMID:25841437
Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. PMID:25814448
Web resources for mass spectrometry-based proteomics. PMID:25721607
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
Phosphoproteomic analysis of the highly-metastatic hepatocellular carcinoma cell line, MHCC97-H. PMID:25690035
PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification. PMID:25653679
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
dbPPT: a comprehensive database of protein phosphorylation in plants. PMID:25534750
Computational methods and opportunities for phosphorylation network medicine. PMID:25530950
Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture. PMID:25420462
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. PMID:25378319
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
Integrating phosphoproteomics in systems biology. PMID:25349677
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Incorporating computational resources in a cancer research program. PMID:25324189
Activation of diverse signalling pathways by oncogenic PIK3CA mutations. PMID:25247763
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. PMID:25122463
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. PMID:25003367
Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. PMID:24981518
Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee. PMID:24904639
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. PMID:24881052
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. PMID:24880689
Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures. PMID:24879340
KinomeXplorer: an integrated platform for kinome biology studies. PMID:24874572
An ensemble method approach to investigate kinase-specific phosphorylation sites. PMID:24872686
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. PMID:24857970
Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects. PMID:24833420
A Proteome-wide Domain-centric Perspective on Protein Phosphorylation. PMID:24830415
Classification of intrinsically disordered regions and proteins. PMID:24773235
Modulation of the chromatin phosphoproteome by the Haspin protein kinase. PMID:24732914
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
Building and exploring an integrated human kinase network: global organization and medical entry points. PMID:24704859
Quantitative phosphoproteomics unravels biased phosphorylation of serotonin 2A receptor at Ser280 by hallucinogenic versus nonhallucinogenic agonists. PMID:24637012
A method for predicting protein-protein interaction types. PMID:24625764
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. PMID:24574112
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. PMID:24564522
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. PMID:24501395
Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PMID:24465218
Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow. PMID:24322422
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
PhosphoNetworks: a database for human phosphorylation networks. PMID:24227675
EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. PMID:24214991
Probabilistic Prediction of Protein Phosphorylation Sites Using Classification Relevance Units Machines. PMID:24163645
Time-scale separation--Michaelis and Menten's old idea, still bearing fruit. PMID:24103070
The mutational landscape of phosphorylation signaling in cancer. PMID:24089029
RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. PMID:24040939
PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites. PMID:23941207
Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors. PMID:23911959
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. PMID:23674503
Distinct types of disorder in the human proteome: functional implications for alternative splicing. PMID:23633940
Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. PMID:23504934
The human leukocyte antigen-presented ligandome of B lymphocytes. PMID:23481700
From Identification to Characterization of the Multiple Sclerosis Susceptibility Gene CLEC16A. PMID:23439554
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
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
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
Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition. PMID:23056474
Quantitative dynamics of phosphoproteome: the devil is in the details. PMID:23020125
CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites. PMID:23001821
Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PMID:22973453
P(3)DB: An Integrated Database for Plant Protein Phosphorylation. PMID:22973285
Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. PMID:22964224
Investigation of receptor interacting protein (RIP3)-dependent protein phosphorylation by quantitative phosphoproteomics. PMID:22942356
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. PMID:22913808
Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. PMID:22899623
Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information. PMID:22889910
Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues. PMID:22889909
Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. PMID:22889908
Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates. PMID:22870394
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
The application of modular protein domains in proteomics. PMID:22710164
A highly scalable peptide-based assay system for proteomics. PMID:22701568
Mapping the stabilome: a novel computational method for classifying metabolic protein stability. PMID:22682214
Linear motifs confer functional diversity onto splice variants. PMID:22638587
iELM--a web server to explore short linear motif-mediated interactions. PMID:22638578
Profile-based short linear protein motif discovery. PMID:22607209
Computational identification and modeling of crosstalk between phosphorylation, O-β-glycosylation and methylation of FoxO3 and implications for cancer therapeutics. PMID:22489133
Efficient motif search in ranked lists and applications to variable gap motifs. PMID:22416066
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. PMID:22373819
Modification site localization scoring: strategies and performance. PMID:22328712
PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. PMID:22182631
Prediction of 492 human protein kinase substrate specificities. PMID:22165948
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. PMID:22159132
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. PMID:22135298
Activity regulation of adenosine deaminases acting on RNA (ADARs). PMID:22113393
ELM--the database of eukaryotic linear motifs. PMID:22110040
Systematic phosphorylation analysis of human mitotic protein complexes. PMID:22067460
Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives. PMID:22009073
Quantitative phosphoproteomics of CXCL12 (SDF-1) signaling. PMID:21949786
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins PubMed citations: 150.

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

KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. PMID:35879309
An atlas of posttranslational modifications on RNA binding proteins. PMID:35438783
Function of BCLAF1 in human disease. PMID:34992690
Individualized Proteogenomics Reveals the Mutational Landscape of Melanoma Patients in Response to Immunotherapy. PMID:34771574
Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. PMID:34673281
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins. PMID:34030700
GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System. PMID:33114312
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
HKPocket: human kinase pocket database for drug design. PMID:31783725
Bioinformatics analysis of capsid protein of different subtypes rabbit hemorrhagic disease virus. PMID:31775738
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PMID:30811403
DeepPhos: prediction of protein phosphorylation sites with deep learning. PMID:30601936
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. PMID:30397019
Heat Shock Protein 90α-Dependent B-Cell-2-Associated Transcription Factor 1 Promotes Hepatocellular Carcinoma Proliferation by Regulating MYC Proto-Oncogene c-MYC mRNA Stability. PMID:30015413
PTM-ssMP: A Web Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile. PMID:29989096
Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. PMID:29920078
A lectin of a non-invasive apple snail as an egg defense against predation alters the rat gut morphophysiology. PMID:29856808
Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management. PMID:29204081
Predicting CK2 beta-dependent substrates using linear patterns. PMID:29124183
Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma. PMID:28932213
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Prediction of post-translational modification sites using multiple kernel support vector machine. PMID:28462053
The T-LAK Cell-originated Protein Kinase Signal Pathway Promotes Colorectal Cancer Metastasis. PMID:28412249
Interrogating the hidden phosphoproteome. PMID:28165663
Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach. PMID:28085066
Association of CTH variant with sinusoidal obstruction syndrome in children receiving intravenous busulfan and cyclophosphamide before hematopoietic stem cell transplantation. PMID:27779248
Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PMID:27336693
The end of a monolith: Deconstructing the Cnn-Polo interaction. PMID:27096551
Phosphorylation of TOPK at Y74, Y272 by Src increases the stability of TOPK and promotes tumorigenesis of colon. PMID:27016416
dbPAF: an integrative database of protein phosphorylation in animals and fungi. PMID:27010073
The Multiple Faces of Disordered Nucleoporins. PMID:26791761
Regulation of lamin properties and functions: does phosphorylation do it all? PMID:26581574
An Amino-Terminal Polo Kinase Interaction Motif Acts in the Regulation of Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila. PMID:26447129
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Mapping of the Sequences Directing Localization of the Drosophila Germ Cell-Expressed Protein (GCE). PMID:26186223
Study of phosphorylation events for cancer diagnoses and treatment. PMID:26055493
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. PMID:25938373
Alternate Phosphorylation/O-GlcNAc Modification on Human Insulin IRSs: A Road towards Impaired Insulin Signaling in Alzheimer and Diabetes. PMID:25580119
Computational methods and opportunities for phosphorylation network medicine. PMID:25530950
Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PMID:25490041
Computational phosphoproteomics: from identification to localization. PMID:25475148
Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds. PMID:25146430
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. PMID:24987309
Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee. PMID:24904639
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. PMID:24771658
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. PMID:24564381
Identification of potential Plk1 targets in a cell-cycle specific proteome through structural dynamics of kinase and Polo box-mediated interactions. PMID:23967120
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
Src activation by β-adrenoreceptors is a key switch for tumour metastasis. PMID:23360994
A rapid screening assay to search for phosphorylated proteins in tissue extracts. PMID:23166814
Prediction of protein phosphorylation sites by using the composition of k-spaced amino acid pairs. PMID:23110047
Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PMID:22973453
Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PMID:22844408
Systematic analysis of protein phosphorylation networks from phosphoproteomic data. PMID:22798277
Counteracting effects operating on Src homology 2 domain-containing protein-tyrosine phosphatase 2 (SHP2) function drive selection of the recurrent Y62D and Y63C substitutions in Noonan syndrome. PMID:22711529
AMS 4.0: consensus prediction of post-translational modifications in protein sequences. PMID:22555647
PhosphoRice: a meta-predictor of rice-specific phosphorylation sites. PMID:22305189
The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. PMID:22194470
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. PMID:22034591
DomPep--a general method for predicting modular domain-mediated protein-protein interactions. PMID:22003397
PChopper: high throughput peptide prediction for MRM/SRM transition design. PMID:21838934
Human linker histones: interplay between phosphorylation and O-β-GlcNAc to mediate chromatin structural modifications. PMID:21749719
Claudin-1 required for HCV virus entry has high potential for phosphorylation and O-glycosylation. PMID:21569618
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. PMID:21552464
Serine 204 phosphorylation and O-β-GlcNAC interplay of IGFBP-6 as therapeutic indicator to regulate IGF-II functions in viral mediated hepatocellular carcinoma. PMID:21548981
Using graph theory to analyze biological networks. PMID:21527005
A quantitative literature-curated gold standard for kinase-substrate pairs. PMID:21492431
dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation. PMID:21466708
Mining recent brain proteomic databases for ion channel phosphosite nuggets. PMID:21149544
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence. PMID:21123182
Identifying human kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources. PMID:21085571
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Global molecular dysfunctions in gastric cancer revealed by an integrated analysis of the phosphoproteome and transcriptome. PMID:20953656
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Phosphoproteomic analysis reveals site-specific changes in GFAP and NDRG2 phosphorylation in frontotemporal lobar degeneration. PMID:20886841
Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. PMID:20688971
T-LAK cell-originated protein kinase (TOPK) phosphorylation of Prx1 at Ser-32 prevents UVB-induced apoptosis in RPMI7951 melanoma cells through the regulation of Prx1 peroxidase activity. PMID:20647304
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. PMID:20631208
SH2 domains recognize contextual peptide sequence information to determine selectivity. PMID:20627867
Modular composition predicts kinase/substrate interactions. PMID:20579376
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. PMID:20492656
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. PMID:20428315
AMS 3.0: prediction of post-translational modifications. PMID:20423529
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. PMID:20122181
AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact of cpCK2 phosphorylation. PMID:20088902
Graphlet kernels for prediction of functional residues in protein structures. PMID:20078397
Understanding protein phosphorylation on a systems level. PMID:20056723
Loss of post-translational modification sites in disease. PMID:19908386
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. PMID:19834895
AntigenDB: an immunoinformatics database of pathogen antigens. PMID:19820110
A proposed syntax for Minimotif Semantics, version 1. PMID:19656396
Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PMID:19649278
Quantitative phosphokinome analysis of the Met pathway activated by the invasin internalin B from Listeria monocytogenes. PMID:19640851
Episodic Src activation in uveal melanoma revealed by kinase activity profiling. PMID:19568237
A comprehensive resource for integrating and displaying protein post-translational modifications. PMID:19549291
Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases. PMID:19494114
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. PMID:19383128
SysPTM: a systematic resource for proteomic research on post-translational modifications. PMID:19366988
The phosphoproteome of bloodstream form Trypanosoma brucei, causative agent of African sleeping sickness. PMID:19346560
KEA: kinase enrichment analysis. PMID:19176546
PhosphoPep--a database of protein phosphorylation sites in model organisms. PMID:19060867
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation. PMID:19000166
Prediction of kinase-specific phosphorylation sites using conditional random fields. PMID:18940828
Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self. PMID:18836451
Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions. PMID:18831792
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains. PMID:18828911
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. PMID:18828897
Cyclin-dependent kinase 1/cyclin B1 phosphorylates varicella-zoster virus IE62 and is incorporated into virions. PMID:18799590
Gain and loss of phosphorylation sites in human cancer. PMID:18689832
PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. PMID:18549264
SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. PMID:18541042
Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry. PMID:18510355
Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. PMID:18501020
The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. PMID:18477637
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. PMID:18463090
Discovering sequence motifs with arbitrary insertions and deletions. PMID:18437229
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. PMID:18424801
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PMID:18389064
Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes. PMID:18372317
Charge environments around phosphorylation sites in proteins. PMID:18366741
Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. PMID:18234718
PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. PMID:18160410
Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. PMID:18079698
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. PMID:18039369
AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update. PMID:17994256
Phospho.ELM: a database of phosphorylation sites--update 2008. PMID:17962309
Systematic discovery of in vivo phosphorylation networks. PMID:17570479
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. PMID:17517770
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. PMID:17478500
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. PMID:17452356
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. PMID:17142231
DILIMOT: discovery of linear motifs in proteins. PMID:16845024
Probabilistic enrichment of phosphopeptides by their mass defect. PMID:16808444
Characterizing the microenvironment surrounding phosphorylated protein sites. PMID:16689688
Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. PMID:16641100
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. PMID:16549034
PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. PMID:16504016
Protein kinases associated with the yeast phosphoproteome. PMID:16445868
dbPTM: an information repository of protein post-translational modification. PMID:16381945
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. PMID:16111488
Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function. PMID:15998447
GPS: a comprehensive www server for phosphorylation sites prediction. PMID:15980451
Phospho.ELM: a database of phosphorylation sites--update 2008 PubMed citations: 121.

121 articles citing: Phospho.ELM: a database of phosphorylation sites--update 2008

KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. PMID:35011609
PARROT is a flexible recurrent neural network framework for analysis of large protein datasets. PMID:34533455
DeepIPs: comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach. PMID:34184738
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
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. PMID:32044914
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. PMID:31848261
HKPocket: human kinase pocket database for drug design. PMID:31783725
The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface. PMID:30567737
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. PMID:30397019
Methods and approaches to disease mechanisms using systems kinomics. PMID:29911197
A 1-phytase type III effector interferes with plant hormone signaling. PMID:29255246
Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management. PMID:29204081
LiverWiki: a wiki-based database for human liver. PMID:29029599
Interrogating the hidden phosphoproteome. PMID:28165663
MicroRNA-140-5p and SMURF1 regulate pulmonary arterial hypertension. PMID:27214554
The end of a monolith: Deconstructing the Cnn-Polo interaction. PMID:27096551
Prediction and verification of novel peptide targets of protein tyrosine phosphatase 1B. PMID:27025565
dbPAF: an integrative database of protein phosphorylation in animals and fungi. PMID:27010073
ERK2 phosphorylation of EBNA1 serine 383 residue is important for EBNA1-dependent transactivation. PMID:27009860
The exploration of network motifs as potential drug targets from post-translational regulatory networks. PMID:26853265
Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PMID:26659599
An Amino-Terminal Polo Kinase Interaction Motif Acts in the Regulation of Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila. PMID:26447129
Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma. PMID:26405815
jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs. PMID:26245277
Study of phosphorylation events for cancer diagnoses and treatment. PMID:26055493
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
Computational methods and opportunities for phosphorylation network medicine. PMID:25530950
Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. PMID:25476580
Cadherin juxtamembrane region derived peptides inhibit TGFβ1 induced gene expression. PMID:25108297
Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee. PMID:24904639
AMASS: a database for investigating protein structures. PMID:24497503
Probabilistic Prediction of Protein Phosphorylation Sites Using Classification Relevance Units Machines. PMID:24163645
Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PMID:24023761
Protein kinase CK2 phosphorylates and activates p21-activated kinase 1. PMID:23885116
Hypoxamirs in Pulmonary Hypertension: Breathing New Life into Pulmonary Vascular Research. PMID:23745175
Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions. PMID:23712012
Missense variants of uncertain significance (VUS) altering the phosphorylation patterns of BRCA1 and BRCA2. PMID:23704879
Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PMID:23690949
The SH2 domain interaction landscape. PMID:23545499
Protein analysis by shotgun/bottom-up proteomics. PMID:23438204
Module cover - a new approach to genotype-phenotype studies. PMID:23424119
Holding our breath: The emerging and anticipated roles of microRNA in pulmonary hypertension. PMID:23130098
Serine phosphorylation is critical for the activation of ubiquitin-specific protease 1 and its interaction with WD40-repeat protein UAF1. PMID:23116119
P(3)DB: An Integrated Database for Plant Protein Phosphorylation. PMID:22973285
Systematic analysis of protein phosphorylation networks from phosphoproteomic data. PMID:22798277
Prioritization of pathogenic mutations in the protein kinase superfamily. PMID:22759651
AMS 4.0: consensus prediction of post-translational modifications in protein sequences. PMID:22555647
A dynamic view of domain-motif interactions. PMID:22253583
Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PMID:22164248
Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PMID:21853102
PChopper: high throughput peptide prediction for MRM/SRM transition design. PMID:21838934
Predicting protein kinase specificity: Predikin update and performance in the DREAM4 challenge. PMID:21829434
MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PMID:21799663
Analysis of EGFR signaling pathway in nasopharyngeal carcinoma cells by quantitative phosphoproteomics. PMID:21711528
PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. PMID:21703007
Discovery of protein phosphorylation motifs through exploratory data analysis. PMID:21647451
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. PMID:21571812
A quantitative literature-curated gold standard for kinase-substrate pairs. PMID:21492431
The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. PMID:21398349
Identifying causal genes and dysregulated pathways in complex diseases. PMID:21390271
Integrative features of the yeast phosphoproteome and protein-protein interaction map. PMID:21298081
Proteomic snapshot of the EGF-induced ubiquitin network. PMID:21245847
The Musite open-source framework for phosphorylation-site prediction. PMID:21210988
Roscovitine inhibits EBNA1 serine 393 phosphorylation, nuclear localization, transcription, and episome maintenance. PMID:21209116
A robust protocol to map binding sites of the 14-3-3 interactome: Cdc25C requires phosphorylation of both S216 and S263 to bind 14-3-3. PMID:21189416
A tissue-specific atlas of mouse protein phosphorylation and expression. PMID:21183079
Mining recent brain proteomic databases for ion channel phosphosite nuggets. PMID:21149544
Systems biology of ageing and longevity. PMID:21115531
Identifying human kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources. PMID:21085571
PHOSIDA 2011: the posttranslational modification database. PMID:21081558
Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity. PMID:21080693
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. PMID:20965970
Global molecular dysfunctions in gastric cancer revealed by an integrated analysis of the phosphoproteome and transcriptome. PMID:20953656
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. PMID:20828632
Viral organization of human proteins. PMID:20827298
A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. PMID:20733106
Chk1-dependent constitutive phosphorylation of BLM helicase at serine 646 decreases after DNA damage. PMID:20719863
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. PMID:20702892
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. PMID:20631208
SH2 domains recognize contextual peptide sequence information to determine selectivity. PMID:20627867
MimoSA: a system for minimotif annotation. PMID:20565705
Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. PMID:20534707
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. PMID:20492656
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. PMID:20459641
AMS 3.0: prediction of post-translational modifications. PMID:20423529
Systems pharmacology of arrhythmias. PMID:20407125
The regulatory crosstalk between kinases and proteases in cancer. PMID:20300104
Feedback between p21 and reactive oxygen production is necessary for cell senescence. PMID:20160708
A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PMID:20126263
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. PMID:20122181
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. PMID:20100358
Understanding protein phosphorylation on a systems level. PMID:20056723
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. PMID:20055997
Phosphoproteomics for the masses. PMID:20047291
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. PMID:19995808
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. PMID:19934261
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. PMID:19879846
A structure filter for the Eukaryotic Linear Motif Resource. PMID:19852836
In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. PMID:19770167
A proposed syntax for Minimotif Semantics, version 1. PMID:19656396
Cellular senescence: unravelling complexity. PMID:19618294
Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PMID:19584925
Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy. PMID:19581576
A comprehensive resource for integrating and displaying protein post-translational modifications. PMID:19549291
An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells. PMID:19534553
Using genome-wide measurements for computational prediction of SH2-peptide interactions. PMID:19502496
Functional organization of the S. cerevisiae phosphorylation network. PMID:19269370
Linear combinations of docking affinities explain quantitative differences in RTK signaling. PMID:19156127
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. PMID:19136663
An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. PMID:19081932
MoKCa database--mutations of kinases in cancer. PMID:18986996
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. PMID:18974045
Prediction of kinase-specific phosphorylation sites using conditional random fields. PMID:18940828
P3DB: a plant protein phosphorylation database. PMID:18931372
Linear motif atlas for phosphorylation-dependent signaling. PMID:18765831
Regulation of innate immune responses by DAI (DLM-1/ZBP1) and other DNA-sensing molecules. PMID:18375758
NetworKIN: a resource for exploring cellular phosphorylation networks. PMID:17981841

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conserved region
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literature curation
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phosphorylation
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literature and language
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sequence analysis
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molecular interactions, pathways and networks
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structure analysis
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conserved region literature curation phosphorylation literature and language sequence analysis molecular interactions, pathways and networks structure analysis

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Phospho.ELM

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Phospho3D

Eukaryotic Linear Motifs

Pf-Phospho

EPSD

Manually Curated Database of Rice Proteins

dbPSP

SELEXdb

ESC

DroID - Drosophila Interactions Database

PhosphoSite Plus

Conserved Domain Database

BIOchemical PathwaY DataBase

Annotated regulatory Binding Sites from Orthologous Promoters

MetaCyc

iUUCD

Yeast KID

GenomeRNAi

FluReassort

Reactome - a curated knowledgebase of biological pathways

Bacterial CSDB (BCSDB)