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Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

https://doi.org/10.1021/acs.jproteome.0c00306

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bip.360221211openalex-snapshot

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

inferredcites →https://doi.org/10.1002/pmic.200300744openalex-snapshot

Unimod: Protein modifications for mass spectrometry

inferredcites →https://doi.org/10.1002/pmic.200401303openalex-snapshot

PRIDE: The proteomics identifications database

inferredcites →https://doi.org/10.1002/pmic.201200232openalex-snapshot

Protein structure as a means to triage proposed PTM sites

inferredcites →https://doi.org/10.1002/prot.21563openalex-snapshot

Prediction of kinase‐specific phosphorylation sites with sequence features by a log‐odds ratio approach

inferredcites →https://doi.org/10.1006/jmbi.1999.3310openalex-snapshot

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

inferredcites →https://doi.org/10.1007/s00726-014-1711-5openalex-snapshot

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

inferredcites →https://doi.org/10.1016/0024-3205(90)90529-zopenalex-snapshot

Evidence that the reversible MAO-A inhibitor moclobemide increases prolactin secretion by a serotonergic mechanism in healthy male volunteers

inferredcites →https://doi.org/10.1016/j.cell.2009.10.006openalex-snapshot

Serine/Threonine Phosphatases: Mechanism through Structure

inferredcites →https://doi.org/10.1016/j.cell.2012.05.036openalex-snapshot

Systematic Functional Prioritization of Protein Posttranslational Modifications

inferredcites →https://doi.org/10.1016/j.jmb.2007.05.022openalex-snapshot

Inference of Macromolecular Assemblies from Crystalline State

inferredcites →https://doi.org/10.1016/j.jprot.2015.07.006openalex-snapshot

ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects

inferredcites →https://doi.org/10.1016/j.str.2011.09.021openalex-snapshot

Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

inferredcites →https://doi.org/10.1016/j.tem.2015.09.013openalex-snapshot

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

inferredcites →https://doi.org/10.1016/j.tibs.2017.01.001openalex-snapshot

A Golden Age for Working with Public Proteomics Data

inferredcites →https://doi.org/10.1016/j.tig.2009.03.003openalex-snapshot

Weak functional constraints on phosphoproteomes

inferredcites →https://doi.org/10.1021/acs.jproteome.7b00085openalex-snapshot

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products

inferredcites →https://doi.org/10.1021/acs.jproteome.9b00328openalex-snapshot

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

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inferredcites →https://doi.org/10.1021/pr200611nopenalex-snapshot

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inferredcites →https://doi.org/10.1038/ncb0502-e127openalex-snapshot

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inferredcites →https://doi.org/10.1038/npre.2008.2079.1openalex-snapshot

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

inferredcites →https://doi.org/10.1038/nrm2203openalex-snapshot

Mechanisms of specificity in protein phosphorylation

inferredcites →https://doi.org/10.1038/nsmb.1842openalex-snapshot

Post-translational modifications in signal integration

inferredcites →https://doi.org/10.1038/s41598-017-08366-3openalex-snapshot

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins

inferredcites →https://doi.org/10.1038/s41598-018-19744-wopenalex-snapshot

Aminode: Identification of Evolutionary Constraints in the Human Proteome

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dbPAF: an integrative database of protein phosphorylation in animals and fungi

inferredcites →https://doi.org/10.1038/srep24735openalex-snapshot

Prioritizing functional phosphorylation sites based on multiple feature integration

inferredcites →https://doi.org/10.1042/bj20091834openalex-snapshot

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inferredcites →https://doi.org/10.1042/bst0370627openalex-snapshot

The regulation of protein phosphorylation

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inferredcites →https://doi.org/10.1093/bioinformatics/bts541openalex-snapshot

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inferredcites →https://doi.org/10.1093/bioinformatics/btt544openalex-snapshot

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inferredcites →https://doi.org/10.1093/bioinformatics/btx085openalex-snapshot

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inferredcites →https://doi.org/10.1093/molbev/msq090openalex-snapshot

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inferredcites →https://doi.org/10.1093/molbev/msq142openalex-snapshot

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inferredcites →https://doi.org/10.1093/nar/27.1.370openalex-snapshot

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkh253openalex-snapshot

The importance of intrinsic disorder for protein phosphorylation

inferredcites →https://doi.org/10.1093/nar/gkn892openalex-snapshot

Human Protein Reference Database--2009 update

inferredcites →https://doi.org/10.1093/nar/gkq1104openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkq936openalex-snapshot

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites

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PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

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inferredcites →https://doi.org/10.1093/nar/gks1258openalex-snapshot

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inferredcites →https://doi.org/10.1093/nar/gkv402openalex-snapshot

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inferredcites →https://doi.org/10.1098/rstb.2012.0106openalex-snapshot

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inferredcites →https://doi.org/10.1111/j.1365-313x.2005.02613.xopenalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.crmeth.2025.101169openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.131180openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jmb.2025.169164openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.sbi.2023.102640openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.str.2021.06.008openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00206openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00164openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00406openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00644openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jproteome.4c00679openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jproteome.5c00958openalex-snapshot

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inferred← citeshttps://doi.org/10.1038/s41467-023-42543-5openalex-snapshot

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inferred← citeshttps://doi.org/10.1038/s41467-026-75138-xopenalex-snapshot

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inferred← citeshttps://doi.org/10.1042/ebc20230079openalex-snapshot

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inferred← citeshttps://doi.org/10.1080/14789450.2022.2160324openalex-snapshot

Proteomic repository data submission, dissemination, and reuse: key messages

inferred← citeshttps://doi.org/10.1093/bib/bbad090openalex-snapshot

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inferred← citeshttps://doi.org/10.1093/bioadv/vbaf301openalex-snapshot

Perspectives in computational mass spectrometry: recent developments and key challenges

inferred← citeshttps://doi.org/10.1093/gpbjnl/qzaf057openalex-snapshot

EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species

inferred← citeshttps://doi.org/10.1093/nar/gkab1038openalex-snapshot

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inferred← citeshttps://doi.org/10.1093/nar/gkac1040openalex-snapshot

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inferred← citeshttps://doi.org/10.1093/nar/gkae1011openalex-snapshot

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inferred← citeshttps://doi.org/10.1093/nar/gkaf1078openalex-snapshot

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inferred← citeshttps://doi.org/10.1093/nar/gkaf1146openalex-snapshot

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inferred← citeshttps://doi.org/10.1101/2022.11.28.518163openalex-snapshot

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inferred← citeshttps://doi.org/10.1101/2024.10.26.620428openalex-snapshot

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inferred← citeshttps://doi.org/10.3389/fmolb.2022.959956openalex-snapshot

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inferred← citeshttps://doi.org/10.3389/fviro.2025.1501616openalex-snapshot

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inferred← citeshttps://doi.org/10.3390/info16121023openalex-snapshot

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inferred← citeshttps://doi.org/10.64898/2026.07.03.736340openalex-snapshot

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inferred← citeshttps://doi.org/10.64898/2026.08.04.742789openalex-snapshot

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inferred← citeshttps://doi.org/10.64898/2026.09.21.753344openalex-snapshot

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