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  Databases
SwissProt The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data.
Phospho.ELM Phospho.ELM is a database of experimentally verified phosphorylation sites in eukaryotic proteins.
HPRD The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.
PhosphoSitePlus PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs). In addition to providing an extensive, manually curated phosphorylation site database, other commonly studied PTMs are included in PSP.
UbiProt The UbiProt Database project aims to summarize a significant volume of data concerning various protein substrates of ubiquitylation. Each database entry describing particular ubiquitylated protein comprises information about protein properties and sources; ubiquitylation features, including details of respective conjugation cascade; literature reference and links to related databases. All data included were experimentally obtained by research groups from around the world and can be verified using respective references.
dbPTM dbPTM was proposed to integrate experimentally verified PTMs from several databases, and to annotate the predicted PTMs on Swiss-Prot proteins. This update extends dbPTM to a knowledgebase comprisingthe modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains and protein variations.
OGlycBase OGLYCBASE is a revised database of O- and C-glycosylated proteins.
OMIM OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources.
KEGG KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
Pfam A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
PhosPhAt The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.
PhosphoPep PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae). The experimental data was collected and analyzed by the Aebersold group at the Swiss Federal Institute of Technology (ETH) in collaboration with the Functional Genomics Center ( FGCZ ) in Zurich, Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.
PDB PDB database is an information portal to biological macromolecular structures.
Gene Ontology The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.
PTMCode PTMCode is a resource of known and predicted functional associations between protein posttranslational modifications (PTMs). It currently contains 13 different PTM types in proteins from 8 different eukaryotic species. A total of 137 525 sites and 401 688 functional associations in 25 764 proteins can currently be explored.
PTMfunc PTMfunc is a repository of functional predictions for protein post-translational modifications (PTMs).
  Predict Tools
KinasePhos KinasePhos is to computationally predict phosphorylation sites within given protein sequences. The known phosphorylation sites are categorized by substrate sequences and their corresponding protein kinase classes. Profile Hidden Markov Model (HMM) is applied for learning to each group of sequences surrounding to the phosphorylation residues. By comparing to other approaches previously developed, our method has higher accuracy and provides not only the location of the phosphorylation sites, but also the corresponding catalytic protein kinases.
GlycoMod GlycoMod is a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses.
SUMOsp A web server for sumoylation site prediction.
MeMo A web tool for prediction of protein methylation modifications.
NetAcet NetAcet 1.0 server predicts substrates of N-acetyltransferase A (NatA).
LysAcet Prediction of lysine acetylation sites using SVM.
NetPhosK The NetPhosK 1.0 server produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites. Currently NetPhosK covers the following kinases: PKA, PKC, PKG, CKII, Cdc2, CaM-II, ATM, DNA PK, Cdk5, p38 MAPK, GSK3, CKI, PKB, RSK, INSR, EGFR and Src.
Scansite Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
AutoMotif The AutoMotif tool allows for identification of PTM (post-translational modification) sites in proteins based on the SVM based LFM method.
User Interface A general user interface for prediction servers of proteins' post-translational modification sites.
GPI-SOM Identification of GPI-anchor signals by a Kohonen Self Organizing Map.
Sulfinator A server to predict tyrosine sulfation sites in protein sequences.
NetNGlyc The NetNglyc server predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.
NetOGlyc The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
GlycoPP GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s).
GPS-PUP GPS-PUP is a novel computational tool for the prediction of pupylation sites.