General: protein and PTM links
UniProt:The Universal Protein Resource
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Provides information about well-established PTMs for any target protein.
Entrez - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
ModPred: predictor of post-translational modification sites in proteins
ModPred is a sequence-based predictor of potential post-translational modification (PTM) sites in proteins. It consists of 34 ensembles of logistic regression models, trained separately on a combined set of 126,036 non-redundant experimentally verified sites for 23 different modifications, obtained from public databases and an ad-hoc literature search.
Cell, Post-translational modifications: Latest Research from Cell journals
Find the latest high impact articles from the Cell family of journals about an assortment of PTMs. For the latest research on specific PTMs please see the links below.
CPLM (Compendium of Protein Lysine Modifications)
CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs).
ExPASY: Bioinformatics Resource Portal
ExPASY has an array of protein modification resource tools.
SysPTM: A Systematic Resource for Post-Translational Modification
SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools.
Acetylation specific Links
Nature, Acetylation: Latest Research and Reviews
Find the latest high impact articles and reviews from an array of journals about the protein modification, Acetylation.
Cell, Acetylation: Latest Research from Cell journals
Find the latest high impact articles from the Cell family of journals about the protein modification, Acetylation.
WERAM: Writers, Erasers, and Readers of Acetylation and Methylation
WERAM 1.0 is a comprehensive Eukaryotic Writers, Erasers and Readers protein of Histone Acetylation and Methylation system Database for 148 eukaryotic species.
ASEB: A Web Server for KAT-specific Acetylation Site Prediction
Lysine acetylation is one of the important post-translational modifications of both histone and non-histone proteins. Thousands of acetylated proteins are known. However, few lysine acetylation transferases (KAT) responsible for the acetylation of these proteins have been identified. ASEB developed the Acetylation Set Enrichment-Based (ASEB) method to predict the KAT families responsible for a given protein.
LysAcet: Lysine Acetylation Predictor
Reversible acetylation on lysine residues, a crucial post-translational modification (PTM) for both histone and non-histone proteins, governs many central cellular processes. Due to limited data and lack of a clear acetylation consensus sequence, little research has focused on prediction of lysine acetylation sites. Incorporating almost all currently available lysine acetylation information, and using the support vector machine (SVM) method along with coding schema for protein sequence coupling patterns, we propose here a novel lysine acetylation prediction algorithm: LysAcet.
Phosphotyrosine specific links
Nature, Phosphorylation: Latest Research and Reviews
Find the latest high impact articles and reviews from an array of journals about the protein modification, Phosphorylation.
Cell, Phosphorylation: Latest Research from Cell journals
Find the latest high impact articles from the Cell family of journals about the protein modification, Phosphorylation.
PhosphoELM: a database of S/T/Y phosphorylation sites
PhosphoELM is a database of S/T/Y phosphorylation sites.
RegPhos: Regulatory Network in Protein Phosphorylation
RegPhos is a resource to explore the protein kinase-substrate phosphorylation networks in human and mouse.
NetworKIN: explore cellular phosphorylation networks
NetworKIN is a database that allows for the exploration of cellular phosphorylation networks.
GPS 5.0: Computational prediction of phosphorylation sites
GPS 5.0 with novel Peptide Selection and Weight Training methods to improve the prediction performance and robustness. Additionally, more than 6,000 phosphorylation sites were used for training and could predict kinase-specific phosphorylation sites for 464 human PKs in hierarchy.
SUMOylation specific links
Nature, SUMOylation: Latest Research and Reviews
Find the latest high impact articles and reviews from an array of journals about the protein modification, SUMOylation.
Cell, SUMOylation: Latest Research from Cell journals
Find the latest high impact articles from the Cell family of journals about the protein modification, SUMOylation.
GPS-SUMO: Prediction of SUMOylation sites and SUMO-binding motifs
Improved prediction algorithm with added, novel SIMs prediction feature.
JASSA v4: Joined Advanced Sumoylation Site and Sim Analyser
Uses a scoring system based on a position frequency matrix derived from the alignment of experimental SUMOylation sites or SUMO-interacting motifs (SIMs).
Ubiquitination specific links
Nature, Ubiquitylation: Latest Research and Reviews
Find the latest high impact articles and reviews from an array of journals about the protein modification, Ubiquitylation (Ubiquitination).
Cell, Ubiquitination: Latest Research from Cell journals
Find the latest high impact articles from the Cell family of journals about the protein modification, Ubiquitination.
hUbiquitome: A database of human ubiquitination sites and cascades
hUbiquitome is a public resource for the retrieval of experimentally verified human ubiquination enzymes and substrates. It is the first comprehensive database of human ubiqutitination pathway proteins and ubiquitin binding-site sequences which is freely available to academia.
UbPred: predictor of protein ubiquitination sites
UbPred is a random forest-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of 266 non-redundant experimentally verified ubiquitination sites available from our experiments and from two large-scale proteomics studies (Hitchcock, et al., 2003; Peng, et al., 2003).
ESA-UbiSite: A web server for identification of Ubiquitination Sites
Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. In fact, some sites that undergo ubiquitination have not been identified. In this work, we propose an evolutionary screening algorithm (ESA) to select effective negatives from among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy, better than existing prediction methods.