Center for Biological Sequence

SignalP (http //www.cbs.dtu.dk/services/SignalP), site of the Center for Biological Sequence Analisys (CBS) for prediction of the presence and location of signal peptides in given amino acid sequences. 

Two more examples of PTM databases are O-GLYCBASE [67], a database of O-glycosylated proteins (http //www.cbs.dtu.dk/databases/OGLYCBASE/), and PhosphoBase [68], a database of phosphorylation sites in proteins and peptides (http //www.cbs.dtu.dk/databases/PhosphoBase/). Both databases are maintained by the Center for Biological Sequence Analysis (CBS) in Denmark, which also provides prediction servers for both types of modifications (NetOGlyc and NetPhos). 

The Center for Biological Sequence Analysis at the Technical University of Denmark has developed SignalP, a powerful tool for the detection of signal peptides and their... 

A third example may be the quantification of complexity for biological sequences. This area has, of course, been widely investigated by many laboratories. Most closely related to our work is that being done at the National Center for Biotechnology Innovation at NIH. There, Wan and Woot-ton developed a compositional complexity measure for biological sequences in proteins and nucleotide sequences in terms of longest paths on the YDL (Wan and Wooton 2000). It is interesting to note... 

The first resources for computer modeling of protein structure are the nucleic acid and protein sequence databases (see Table 6.1), curated by the European Molecular Biology Laboratory (EMBL) in Europe, the National Center for Biotechnology Information (GenBank at the NCBl) in the United States, and the DNA Database of Japan (DDBJ) in Japan. These databases are accessible via the Internet, and most likely one s own scientific institution maintains a local version, which is updated through CD-ROMs released quarterly. Perhaps the predominant protein sequence database is SWISS-PROT. - Others include the nonredundant protein sequence database (OWL) and the protein identification resource database (PIR). ... 

CDD [24,25] is a database of conserved protein domains associated with particular biological functions, together with tools for identifying such domains in query sequences. This now includes COGs and KOG. According to the National Center for Biotechnology Information (NCBI),... 

The coupling of reaction sequences through the adenylate system is entirely different from the two types of stoichiometric relationships discussed above. The stoichiometry of each reaction in which ATP is regenerated or used is, of course, fixed by the nature of the reaction, but the number and types of reactions in which ATP is involved have been determined by evolutionary processes, rather than by simple chemical necessity. Indeed the use of ATP as a coupling agent and the evolutionary adjustments of stoichiometric relationships for maximal metabolic advantage are at the very center of biological function. This fact is underscored by the participation of ATP in every extended metabolic sequence. 

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