PTM Analysis Resource Portal


dbPTM is updated as an integrated resource for PTMs, providing not only a comprehensive dataset of experimentally verified PTMs that are supported by the literature but also an integrative platform for accessing all available databases and tools that are associated with PTM analysis.

Databases
#Database NameDescriptionURLReference
1GlycoEpitopeCarbohydrate chains occupy truly significant positions in various fields of life sciences and biotechnology. Recently, the wide-ranging involvement of carbohydrate chains in life sciences has been extended to such diverse functions as cell to cell recognition and communication in neuronal tissues and immune systems, pathogen recognition, sperm-egg recognition and fertilization, regulating hormonal half-lives in the blood, directing embryonic development and differentiation, and directing distribution of various cells and proteins throughout the body. A large number of polyclonal or monoclonal antibodies have been used as very important tools for analyzing expression of various carbohydrate chains and their functions. In this database, useful information on these carbohydrate antigens, i.e. glyco-epitopes, and antibodies has been assembled as a compact encyclopedia.http://www.glycoepitope.jp/
2GlycomeDBCarbohydrates are the third major class of biological macromolecules, besides proteins and DNA molecules. They are involved in numerous biological processes, among them protein folding and inter/intra cell recognition. In contrast to DNA and proteins neither a comprehensive database for carbohydrate structures nor a universal nomenclature for computational purposes exists. After the cease of funding for the Complex Carbohydrate Structure Database (CCSDB, often referred as CarbBank) in 1997, four initiatives developed independent databases with partially overlapping foci. For each database, a proprietary encoding scheme for residues and topology of the structures was designed. As a result it is virtually impossible to get an overview of all existing structures, and to compare the contents of the different databases. We have analysed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases.http://www.glycome-db.org/21045056
3UnicarbKBUniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.http://unicarbkb.org24234447
4GLYCOSCIENCES.deThe human genome seems to encode for not more than 30,000 to 40,000 proteins. A major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. The importance of protein glycosylation is becoming widely realized through studies on protein folding, protein localization and trafficking, protein solubility, biological half-life as well as studies on cell-cell interactions. The progressing Glycomics projects will dramatically accelerate the understanding of the roles of carbohydrates in cell communication and lead to novel therapeutic approaches for treatment of human disease. The MIT's magazine of innovation (January 21 2003) has identified Glycomics as one of the top ten technologies that will change the future.http://www.glycosciences.de/16239495
5GlycoSuiteDBUniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.http://www.unicarbkb.org/12520065
6CFGThe CFG's Glycan Structures Database offers detailed structural and chemical information for thousands of glycans, including both synthetic glycans and glycans isolated from biological sources. Each glycan structure in the database is linked to relevant entries in CFG and external databases (including primary data and information about binding proteins, where available). Links are also provided to a 3-D modeling feature, references, and other information.http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp25753711
7ProGlycProtProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. ProGlycProt is an extensive online collection of experimentally verified glycosites and glycoproteins of the prokaryotes. For users’ benefit, the database under menu ProGlycProtdb is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoprote