Biology Reference
In-Depth Information
2.3. SWISS-MODEL Server and Workspace
Since its outset, the aim of SWISS-MODEL has been to provide a user-
friendly interface for fully automated, high-quality protein structure
models. With advancing technology, the user interface of SWISS-
MODEL has evolved from the first e-mail protein modeling service
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—
over a web-based submission system on ExPASy, the first Internet web
server dedicated to molecular biology
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— to an interactive web-based
modeling expert system.
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Today, SWISS-MODEL Workspace offers for
each user a personal web-based integrated working environment where
several modeling projects can be carried out in parallel. Protein sequence
and structure databases necessary for modeling are accessible; and tools
for template selection, model building, and structure quality evaluation
can be invoked from within this Workspace.
Depending on the difficulty of the individual modeling task, the
Workspace assists the user in building and evaluating protein homology
models at different levels of complexity. For models that can be built
based on sufficiently similar templates, we provide a fully automated mode
where no user input, other than the sequence of the protein to model, is
required. This is, of course, the easiest and most user-friendly way to
obtain a protein model. On the other hand, for more difficult modeling
scenarios with less target-template sequence similarity, the user is given
control over individual steps of model building: functional domains in
multi-domain proteins can be detected, secondary structure and disor-
dered regions can be predicted for the target sequence, suitable template
structures can be identified by searching the SMTL, and target-template
alignments can be manually adjusted. The program DeepView
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is tightly
linked to SWISS-MODEL, and allows the visualization and manipulation
of modeling projects. As quality evaluation is indispensable for a predic-
tive method like homology modeling, several quality checks are available
to assess the expected accuracy of the models. All relevant data of a mod-
eling project are presented in a graphical synopsis.
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2.4. SWISS-MODEL Repository
The aim of the SWISS-MODEL Repository is to provide access to an
up-to-date collection of high-quality annotated models generated by
