Database Swiss-Model

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

Fig. 1. Comparison of the three-dimensional structures of human Interleukin-8 (green) MCP-1 (blue) and Fractalkine (EST Z44443) (red). The 11-8 structure is taken from the Protein Database (PDB) entry (1IL8), and the MCP-1 structure is a model built of the NMR structure of MI P-l (> (PDB entry 1HUM). The intrachain disulfide bonds are shown in yellow. The model for the chemokine domain of Fractalkine was built using the SwissModel server (16,17). As can be seen the three structures show a large degree of conservation of the overall structure, despite a relatively low level of primary sequence identity. The additional three amino acids in Fractalkine are accommodated as a 310 helix between the two N-terminal cysteines. The steric requirements here presumably forbid a CX2C motif. The model building software can be accessed at http www.expasy.ch swissmod SWISS-MODEL.html...

The ExPASy Proteomic Server (http //www.expasy.org) or its mirror site (e.g. http //us.expasy.org in U.S.A. and http //ca.expay.org in Canada) provides comprehensive resources and tools for proteomic analyses. They include Databases (e.g. Swiss-Prot, Prosite, Enzyme), Tools (e.g. BLAST, ProtParam, ProtScale, SIM, SWISS-MODEL, Translate), Services (e.g. ExPASy ftp server, BioHunt, 2D Hunt), Documentation and links. 

SWISS-PROT sequence database, Swissmodel homology modeling, etc. ExPASy http //expasy.hcuge,ch/... 

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). ... 

Apart from complete modeling packages (discussed below), only a small number of programs are freely and publicly available from the many methods that have been published (see Table 5.6). Among database methods, this includes only Swiss-PDBViewer [151], and BRAGI which implements the method of Fechteler et al. [128]. Several loop databases are available. Among... 

D. Appel, D. F. Hochstrasser. Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases the example of Escherichia coli. Electrophoresis. 

For each reaction in the generated pathway, users can manually select the reactions to be represented by dynamic equations. InitiaUy, the GEM system would automatically search for static reactions based on monomer enzymes found in Brenda and Swiss-PROT databases. Based on the search results, the static part of the model is then generated using the hybrid dynamic/static simulation algorithm detailed below. Finally, the generated pathway model can be used for simulations in E-Ccll System. Users can then specify dynamic equations by selecting an appropriate reaction mechanism and input reaction parameters, or they can program their own set of reaction process description files. 

Table3 Further hydration and volume data (Si, V) for anhydrous and hydrated proteins as obtained by simple calculation procedures, together with some secondary parameters (V/M, Ny,/S, Vw(2rw) /5 ). Calculation procedures hydration Si according to Kuntz (K) volumes V according to Traube (T) or Cohn and Edsall (CE) these calculations were performed without ligands, using the molar masses M from the SWISS-PROT database (Table 1). Volumes V obtained by the programs SIMS (Table 1) or HYDCRYST (HC) and/or HYD-MODEL (HM) (Table 2) are inclusive of the contributions of ligands for calculating the V/M ratios, the molar masses from the crystal structure (Mcryst, Table 2) were used if these were different from the SWISS-PROT data...

The Swiss approach is sometimes exclusively mentioned in major textbooks which deal with aqueous chemistry oriented toward the environment and has also influenced the choice of the model in a widely appreciated book, whereby the first self-consistent surface complexation database was established by Dzombak and Morel for hydrous ferric oxide (2-line ferrihydrite) [76]. This book has been of major influence in particular for users, who find the database that... 

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