SWISS-MODEL

Peitsch M C1996. ProMod and Swiss-Model Intemet-tased Tools for Automated Comparative Pro Modelling. Biochemical Society Transactions 24 274-279. 

SWISS-MODEL http //www.expasy.ch/swissmod/SWISS-MODEL.html... 

MC Peitsch. PROMOD and SWISS-MODEL Internet-based tools for automated comparative protein modeling. Biochem Soc Trans 24 274-279, 1996. 

Schwede T., Diemand A., Guex N., and Peitsch M. C. (2000) Protein structure computing in the genomic era. Res. Microbiol. 151, 107-112. http //www.expasy.ch/swissmod/SWISS-MODEL.html. 

Board of the Swiss Federal Institutes of Technology (1998). 2000 Watt Society - Swiss Model. Sustainability Strategy within the Swiss Institutes of Technology (in German). Wirtschaftsplattform. ETH Zurich. 

Fragment-assembly approach, such as Composer [18] or SWISS-MODEL [19]... 

Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-PdbViewer an environment for comparative protein modeling. Electrophoresis 18 2714-2723. 

Peitsch MC. 1996. ProMod and Swiss-Model internet-based tools for automated comparative protein modeUing. Bio-chem Soc Trans 24(1) 274-279. 

Programs for the prediction of 3-D stracture usually use available protein domains from PDB see Table 1.1) as templates. Tools that are nsually used include SWISS-MODEL see Table 1.1). The query result includes the template used, the ahgnment between the query sequence and the template, and the predicted 3-D model. 

Swiss-Model (An Automated Knowledge-Based Protein Modelling Server)... 

Homology model and putative active center Using the program SWISS Model a homology model of IwHNL was created using the 3D structures of similar en-... 

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. 

Save the trial structure (File -> Save -> Layer) as trialmol.pdb, which can be submitted to Swiss-Model (http //www.expasy.ch/swissmod/) using Optimise (project) mode for optimization. 

Schwede T, Kopp J, Guex N et al, SWISS-MODEL an automated protein homology-modeling server. Nucleic Acids Res 2003 31 3381-3385. 

Use the SWISS-MODEL (9) to build possible protein structures for these genes dock potential broad-spectrum antibiotics candidates to the active sites with AutoDock (10) and use molecular dynamics simulations to research possible binding modes between antibiotics and target proteins (11). 

Go to the SWISS-MODEL Web site (http //www.swissmodel. expasy.org), select Automated Mode, input the e-mail address and the amino acid sequence of the protein retrieved from the Protein Information table, and click Submit Modeling Request to build target protein structure. (See the crystal structure of SpoVT AbrB (pdb code 2W1T) for Bacillus subtilis in Fig. 1.)... 

Arnold K, Bordoli L, Kopp J et al (2006) The SWISS-MODEL workspace a web-based environment for protein structure homology modelling. Bioinformatics 22 195-201... 

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...

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