SKPDB: a structural database of shikimate pathway enzymes

Abstract

BackgroundThe functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.DescriptionThe ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.ConclusionsThe SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/.

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

“…Especially the large LipidBlast library of over 200,000 MS/MS spectra of complex lipids is a good example how rule-based generation of virtual spectra may upend the dominance of small reference spectral libraries used in metabolomics [53]. Computational MS is a necessity for big data initiatives involving MS/MS and MS n analyses and fragmentation trees [36,51,54,55]. Use of such tools is evaluated in a new initiative, the Critical Assessment of Small Molecule Identification contest (CASMI) [56,57].…”

“…MetFrag was developed to generate all in-silico fragments using a bond-disconnection method [54] and was reviewed [26,74,75]. MetFrag generates fragmentation trees to reduce the number of calculated fragments.…”

“…They are taken into account when the scores of all in-silico candidate fragments are computed. MetFrag is limited to accurate mass data and performs best when generating a fragmentation tree with a maximum depth of 2 [54]. Subsequently, MetFusion was developed to improve compound identification by combining both MetFrag and mass spectral searching in MassBank [76].…”

Using Threads to Overcome Synchronization Delays in Parallel Multiple Progressive Alignment Algorithms

“…More different approaches includes the inversion of the conventional order for progressive alignment, as proposed by (Kleinjung et al, 2002), use of decentralized cache (Trystram and Zola, 2005), protein foldings (Palu et al, 2007;Arcuri et al 2010).…”

Emerging trends in research on spatial and temporal organization of terpenoid indole alkaloid pathway in Catharanthus roseus: a literature update

“…The shikimate pathway leads to the formation of aromatic amino acid tryptophan which serves as the sole donor of indole ring to a variety of plant metabolites including auxins, glucosinolates, phytoalexins, TIAs, etc. (Herrmann 1995;Knaggs 2001;Arcuri et al 2010). Anthranilate synthase (AS), which is a key regulatory enzyme associated with tryptophan synthesis from chorismate, is strongly feedback inhibited by tryptophan which binds to an allosteric site on the AS catalytic α-subunit (Radwanski and Last 1995).…”