Provides information and resources to facilitate phosphorylation research. PhosphoSite is a curated database dedicated to aggregating information on physiological protein phosphorylation sites. Its goal is to identify and organize information about all in vivo phosphorylation sites in human and mouse proteomes. It contains over 330 000 non-redundant post-translational modifications (PTMs), including phospho, acetyl, ubiquityl and methyl groups.
Provides access to experimentally derived information about the human proteome including protein–protein interactions (PPIs), post-translational modifications (PTMs) and tissue expression. HPRD is an integrated knowledgebase for genomic and proteomic investigators. The database also includes (i) PhosphoMotif Finder that contains known kinase/phosphatase substrate and binding motifs, (ii) links to a signaling pathway resource called NetPath, (iii) a distributed annotation system, called Human Proteinpedia for enhanced community participation and allows the use of BLAST for querying mRNA/protein data.
Stores experimentally verified phosphorylation sites in eukaryotic proteins. Phospho.ELM is a manually curated web-based resource that contains more than 42 000 non-redundant instances of phosphorylated residues in more than 11 000 different protein sequences (tyrosine, serine and threonine residues). The database also provides links to other resources. Users can participate in the curation of the Phospho.ELM resource by submitting their own data.
An open access database for storage, sharing and visualization of data related with the human T-lymphocyte phosphoproteome. LymPHOS aims to provide a complete set of experimental data including chromatographic and spectrometric information. Current release 2.0 contains 15 566 phosphorylation sites from 8273 unique phosphopeptides and 4937 proteins, which correspond to a 45-fold increase over the original database description. All MS2 and MS3 spectra justifying a p-site assignation are provided together with the corresponding Sequest, OMSSA, Phenyx, Peaks or EasyProt identification scores and p-site assignation scores (Q-Ascore). LymPHOS now includes quantitative data on phosphorylation changes after time-dependent treatment with activators of the TCR-mediated signal transduction pathway. Sequence data quality has also been improved with the use of multiple search engines for database searching. The web-based user interface allows searching phosphorylation sites on specific proteins and/or peptides as well as browsing the entire database, in all cases having experimental data to support each phosphorylation site assignment.
Allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest. PHOSIDA lists posttranslational modification sites associated with particular projects and proteomes or, alternatively, displays posttranslational modifications found for any protein or protein group of interest. In addition, structural and evolutionary information on each modified protein and posttranslational modification site is integrated. Importantly, Phosida links extensive peptide information to the sites, such as several peptides implicating the same site and temporal profiles of each site in response to stimulus (e.g., EGF stimulation).
Supplies a repository composed of 3D structures of phosphorylation sites (P-sites) stemmed from the Phospho.ELM database. Phospho3D enhances data from the previous database at the residue level with annotations and structural information. Moreover, it gathers results of a large-scale structural comparison procedure to allow identification of new putative phosphorylation sites. Additionally, it offers a tool which permit to compare a protein structure to the collected dataset.
Supplies information about phosphopeptides which were identified from Arabidopsis and rice cells by liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS)-based shotgun phosphoproteomics approach. The RIPP-DB allows users to predict conserved phosphorylation sites in plants thanks to alignment views of orthologous proteins in Arabidopsis and rice mapped with the identified phosphopeptides. Data statistics are available directly on the homepage. These contents can be downloaded by users.
Provides phosphorylated sites for kinases. KANPHOS offers a tuple of a kinase, its substrate, the extracellular signal for the phosphorylation, and the experimental condition used for the identification. It permits users to search data in three ways: (1) searching for substrates phosphorylated by a specific kinase; (2) searching for kinases phosphorylating a specific protein; and (3) searching for kinases and their target substrates involved in a specific signaling pathway.
A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
Gathers phosphoproteomic data from total inner medullary collecting duct (IMCD) cell lysates. More specifically, CDPD is a repository that contains data from IMCD cells purified from rat inner medullas. The online interface of the database supplies several types of information such as: protein annotation, RefSeq number, gene symbol, residue, experiment, or sequence.
Provides a resource of protein phosphorylation data from multiple plants. With the large-scale phosphorylation data and associated web-based tools, P3DB will be a valuable resource for both plant and nonplant biologists in the field of protein phosphorylation.
Permits users to visualize genome mutations in gene and protein networks. ActiveDriverDB is a proteo-genomics resource for interpreting human genome variation using post-translational modification (PTM) sites. Novice users can start from example queries of well-annotated genes. Users can also interpret candidate variants from DNA sequencing experiments and compare it with existing public datasets as well as run an automatically analysis of specific variants. Besides, it includes various search options and can generate export tables, upload and publication-quality figures.
Integrates two kinds of high-throughput phosphorylation data, protein microarray-verified kinase–substrate relationships (KSRs) and mass spectrometry (MS)-verified phosphorylation sites. Relative to other human phosphorylation-related databases, such as Phospho.ELM, PhosphoNetworks has three significant merits. First, it is a high-resolution phosphorylation network database, which connects kinases not only to their downstream substrates but also at specific phosphorylation sites on the substrates. Second, it covers a far greater number of novel identified KSRs (24 046 raw KSRs and 3656 refined KSRs) and novel predicted phosphorylation motifs (300 motifs, over double that of the previous knowledgebase). Finally, it provides some unique tools to make it easier for the user to explore and analyze the data.
A compartment-wide map of phosphorylation sites from eight human subcellular compartments analyzed by proteomic characterizations. 10,265 phosphorylation proteins are collected for different subcellular compartments. This data set reveals that the subcellular phosphorylation distribution is compartment-type dependent and that phosphorylation displays site-specific sequence motifs that diverge between subcellular compartments.
Gathers experimentally verified in vivo phosphorylation sites in the Saccharomyces cerevisiae proteome. PhosphoGRID is an online database that represents a substantial expansion of the phosphosite data set, as derived from both high-throughput (HTP) and low-throughput (LTP) studies. It incorporates over 1614 unique phosphosites derived from LTP studies. The data contained in this repository assist users in the prediction of new network elements and information flow, in the form of regulated phosphorylation events.
Allows users to search and find motifs with any sequence data set. scan-x is made to take output of motif-x and scan protein sequence files for the occurrences of these motifs in other proteins or proteomes. It uses fixed residues as a pattern to search within protein sequence files, and matches sequences that contain some patterns. The web interface offers users to realize a research from several dataset.
A curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. dbPAF is useful for further analyses of protein phosphorylation in human and other model organisms.
Gathers information about mass spectrometry (MS)/MS spectra. PepBase is a peptide database that consists in a grouping of experimental data handled by a single analytical platform at the proteomics laboratory of IAB.
Provides a searchable platform for retrieval of information regarding structure similarity, function and published literature about Plasmodium kinases and phosphatases. KiPho is a web resource provides PubMed link and google scholar link for research and review articles related to the query proteins, published till date. It uses scripts, which in turn uses Boolean logic search that includes its name, protein, new and old IDs assigned to it. This method helps the user to find all updated query protein-related publications.
Comprises high-confidence in vivo phosphosites identified by MS-based proteomics in various fungal species. FPD contains 62,272 non-redundant phosphorylation sites in 11,222 proteins across eight organisms, including Aspergillus flavus, Aspergillus nidulans, Fusarium graminearum, Magnaporthe oryzae, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Cryptococcus neoformans.
A curated database of phosphorylation sites in prokaryotes for 96 prokaryotic organisms, which belong to 11 phyla in two domains including bacteria and archaea. All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options. The dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes.
A project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from four different organisms. Currently the database hosts phosphorylation data from the fly, human, worm, and yeast.
Provides user-friendly accession of phosphoproteome in testis. pTestis is a database that integrates all of the identified phosphorylation sites along with UniProt annotations into the database, with snapshots. Users can quickly perform various searches such as a keyword-based query and sequence-based blast. It also offers in vivo Group-based Prediction System (iGPS) prediction results, which presents potential kinase-substrate regulatory relationships.
A comprehensive database which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82 175 phosphorylation sites in 31 012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community.
A tool exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. PFP focused on evaluating the intrinsic characteristics of functional phosphosites and predicting whether a phosphosite is likely to be functional using multiple integrated characteristics. Features including conservation, kinase association and structure information were explored and compared in both known functional and background phosphosite datasets. The two datasets were classified by several trained classifiers based on feature integration.
A database for human phosphovariants. PhosphoVariant can be used in pathophysiological studies of mutations and in the selection of polymorphisms of clinical and phenotypical importance. The screening and prediction of phosphovariants can be a starting point for further research.
Provides a resource for persons seeking an entry into an emerging area of interest. The Phosphorylation Site Database is an online resource that: (i) provides content of significant utility not readily obtainable from other sources, (iii) reports information derived from accessible, verifiable sources, (iv) compiles pertinent information in a succinct format, (v) is readily searched using a variety of criteria, (vi) links users to sources of both supporting documentation and pertinent supplementary information.
It was utilized to investigate the influence of the surrounding amino acids of post-translationally and co-translationally modifiable sites. It has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post-translational modifications (PTMs).
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.