9 The SWISS-MODEL server

The aim of the Internet-based SWISS-MODEL server is to provide an automated, easy to use, web-based comparative protein modelling workbench.

URL: http://swissmodel.expasy.org 

SWISS-MODEL Workspace

is reachable on the World Wide Web (WWW) and requests can be submitted through easy to fill forms. Since protein modelling is heavily dependent on the alignment between target and template sequences, SWISS-MODEL provides four distinct modes of function accessible through separate forms:

  1. The First Approach Mode: This mode allows the user to submit a sequence or its Swiss-Prot identification code. In this mode, SWISS-MODEL will go through the complete procedure described above. The First Approach Mode also allows the user to define a choice of pre-selected template structures, thereby overruling the automated selection procedure. The results of the modelling procedure will be returned to the user via E-mail.
  2. The Project Mode allows the user to re-compute a model by submitting altered sequence alignments and ProMod command files. The sequence alignment procedure, which is fully automatic in the First Approach Mode, may yield sub-optimal alignments and consequently lead to erroneous models. The automated alignment of moderately similar sequences is indeed often imprecise and the boundaries of non-conserved loops are frequently ill defined and miss-aligned. These regions of the sequence alignments must therefore be corrected by hand in order to overcome these weaknesses. The Optimise Mode allows the user to do such corrections, and to request the remodelling of the sequence by submitting his own sequence alignment. This is best done by preparing a modelling request within the Swiss-PdbViewer (see chapter 12). These requests can then be saved as "HTML" files and then submitted through a Web browser.
  3. Alignment Mode: If the three-dimensional structure is known for at least one of the members, this alignment can be used as starting point for comparative modelling using the "alignment mode". The "alignment mode" allows the user to test several alternative alignments and evaluate the quality of the resulting models in order to achieve an optimal result.

The SWISS-MODEL Web interface provides help and guidelines to the use of the difference server modes.

SWISS-MODEL Repository

 

 

 

Last modification: Please note that these pages have not been updated since 1999 and are provided on a "as is basis". We are currently working on an updated version of this course.