SWISS-MODEL WORKSPACE TUTORIAL

   
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How do I use the fully automatic mode of SWISS-MODEL workspace?

The "automated mode" is suited for cases where the target-template similarity is sufficiently high to allow for fully automated modelling. As a rule of thumb, automated sequence alignments are sufficiently reliable when target and template share more than 50% percent of sequence identity.

 

This submission requires only the amino acid sequence (FASTA format or single letter raw sequence) or the UniProt accession code of the target protein as input data. The modelling pipeline automatically selects suitable templates based on a Blast E-value limit, which can be adjusted upon submission (Altschul et al.). The automated template selection will favour high-resolution template structures with reasonable stereochemical properties as assessed by ANOLEA mean force potential (Melo et al.) and Gromos96 force field energy (van Gunsteren et al.).

Example: Modelling the catalytic domain of Cyclodextrin glucanotransferase from Bacillus stearothermophilus (UniProt AC code: Q9ZAQ0).

[ Modelling ] [ Automated Mode ]

Note: Workunits will be automatically deleted after 1 week from the server. When the modelling project is finished, please download the results and save them locally:

  • Model coordinate file (PDB format or DeepView project format) PDB files can be displayed using DeepView, Dino, or otehr tools for molecular visualization.
  • Logfile PDF: The content of the web page (including images and logfiles, but not the model coordinates) can be downloaded and saved as PDF. See "Print this page [pdf]" at the top of the page. PDF files can be displayed using Acrobat Reader.

 


 

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