Introduction

The SWISS-MODEL Workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity.

Successful model building requires at least one experimentally determined 3D structure (template) that shows significant amino acid sequence similarity with the target sequence. Building a homology model comprises four main steps: identification of structural template(s), alignment of target sequence and template structure(s), model building, and model quality evaluation. These steps can be repeated until a satisfying modelling result is achieved. Each of the four steps requires specialized software and access to up-to-date protein sequence and structure databases.

Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Software tools for template selection, model building, and structure quality evaluation can be invoked from within the workspace. A personal working environment (workspace), where several modelling projects can be carried out in parallel, is provided for each user.

The following tutorial aims to facilitate the first steps of working with SWISS-MODEL Workspace. Please let us know if you would like to see other features explained in this tutorial (help-swissmodel@unibas.ch).

How do I work with SWISS-MODEL workspace ?

• How can I create an account?
• How can I manage my projects?

How can I build an homology model using SWISS-MODEL workspace ?

• My protein is quite large, and would like to identify individual domains I could model separately.
• If I have no idea about possible templates for my target, and
  • I want to identify possible templates.
  • I want to try the fully the automatic mode.
• I already have a target-template alignment and want to model my protein
  • by using the alignment submission tool.
  • by visually verifying the alignment in DeepView.

How can I assess protein structure model quality ?

• What accuracy can I expect for a model build by the automated mode of SWISS-MODEL?
• How can I assess protein structure model quality with empirical force-field and Mean Force Potential methods?
• How can I assess geomoetrical accuracy of a structure or model?