Biology Reference
In-Depth Information
automated homology modeling, bridging the gap between sequence
and structure databases. All models in the Repository are publicly
accessible via an interactive website. The current release provides
more than 1.3 million annotated 3D models. The SWISS-MODEL
Repository is cross-referenced with UniProt and InterPro, comple-
menting the structural information available in these two databases.
Each entry in the Repository contains a sequence-based checksum,
which uniquely identifies its corresponding target amino acid sequence
and guarantees data consistency when exchanging records between dif-
ferent databases to ensure that hyperlinks between websites using data-
base accession codes are referencing identical protein sequences.
We have extended this concept to generate a common protein refer-
ence for protein models, which allowed us to build a single protein
model portal (see below).
Each target sequence in the Repository has a short protein descrip-
tion with links to relevant sequence-based resources. A graphical repre-
sentation of the InterPro functional and domain-level annotations of the
target sequence indicates regions of functional and structural importance
in the target sequence. Their location relative to the available models can
be visualized directly from the website, or using external visualizing tools
such as DeepView.
2.5. SWISS-MODEL and DeepView —
Swiss-PdbViewer
DeepView
12
— aka Swiss-PdbViewer — is a powerful graphical tool for
protein structure visualization, analysis, and manipulation, and can be used
as a graphical front-end to SWISS-MODEL Workspace. In cases where
automated sequence alignment fails to accurately position insertions and
deletions in the target-template alignment, one can often optimize the
model by manually altering the alignment in these regions. DeepView
allows one to visually inspect these regions of interest, manipulate the
alignment (or invoke a search for alternative templates), and submit a new
model request to SWISS-MODEL Workspace. In combination, DeepView
and SWISS-MODEL are forming a powerful integrated sequence to struc-
ture workbench. The program can be downloaded freely from the ExPASy
server for Windows™ and Macintosh™ platforms.
