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SWISS-MODEL Repository Help

Introduction to SWISS-MODEL Repository

The SWISS-MODEL Repository (SMR) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. It provides access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant model organisms. Currently, models are provided for the reference proteomes of 12 model organisms, based on UniProtKB release 2017_04. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline is fully utilised.

Users can assess the quality of the models in the database, search for alternative template structures, and build models interactively via SWISS-MODEL Workspace. Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal facilitates the navigation between protein sequence and structure resources.

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

Bienert S, Waterhouse A, de Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T (2017). The SWISS-MODEL Repository - new features and functionality Nucleic Acids Res. 45(D1):D313-D319.

Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res. 45(D1):D313-D319.


Data content and update

SMR currently provide models for the Swiss-Prot section of UniProtKB and for the reference proteomes of the following model organisms: H. sapiens, M. musculus, C. elegans, E. coli K12, A. thaliana, D. melanogaster, S. cerevisiae, Caulobacter crescentus, M. tuberculosis, P. aeruginosa, Staphylococcus aureus and P. falciparum.

For each core species proteome, SMR provides a dedicated summary page with information on the target proteome, statistics on model coverage as well as the analysis of structural coverage of the proteome over time.

The full set of model data for each core species is downloadable from the main entry page as well as the summary page. Models for non-core sequences are added on demand by interactive user request.

A continuous release mechanism ensures that the models are regularly updated based on the latest template information and the latest version of the SWISS-MODEL modelling pipeline. The current version of the SMR features a three-tiered policy for updating: monthly, weekly and on-demand.

Monthly updates are initiated when a new version of UniProtKB is released, i.e. the amino acid sequences of UniProtKB entries may have changed or the composition of the core species proteomes may have been updated.

Weekly updates ensure that the latest PDB release is readily integrated in the SWISS MODEL Template Library (SMTL), and models are built using the latest template information.

On-demand updates are meant for sequences that are not part of the core species data set. When accessing an SMR entry for which no models have been built, or the existing models are not based on current template information, the user is presented with two options: (i) requesting an automated update of the SMR entry (ii) starting an interactive modelling job on SWISS-MODEL Workspace.


Accessing data

The SMR web interface provides several entry points for accessing the data. The simplest way to directly access an entry is via its UniProtKB accession code. Alternatively, free text search on protein names, functional description and organisms allows selecting entries from a list of results matching the search keywords.

The main page offers a general summary about the repository content and, for each of the core species, the following information: total number of canonical sequences in the reference proteome (according to UniProtKB), number of sequences for which at least one model is present, total number of models for that species, a sequence coverage plot showing the number of sequences that have models or structures in a certain sequence coverage range (>80%, between 60% and 80%, etc.). A colour gradient, from dark green to red, specifies different coverage values, from high to low respectively. The size of each box is proportional to the number of target sequences within a given range of coverage (i.e., for E. Coli, more than 60% of the proteins are covered by more than 80% over their sequence length by structures and models, as of march 2017).

A download button allows to download all the metadata about models and structures of a given core species (further details are provided in the help file in the downloaded folder as well as in the “SMR API” section below).


Model species page

By clicking on the core species names the user can access a dedicated summary page, with information on the target proteome, statistics on model coverage as well as the evolution of structural coverage of the proteome over time. The full set of model data for each core species is downloadable from the main entry page as well as the summary page.


SWISS-MODEL Repository entry page

Individual entries can be searched via UniProtKB accession codes or using a free text search on protein names, functional description and/or organisms. In the latter case the user is provided with a list of entries matching the search keywords and access the information of each entry by selecting from the list.

The entry view page for a specific entry provides four general sections: (i) a graphical representation of the target coverage by models and experimental structures, (ii) a SMR entry summary, (iii) a 3D structure visualization of the entry and (iv) the target-template sequence alignment. Each of these sections is described below.


Structural coverage

The amino acid sequence of the target is indicated as a gray arc. The information of the structural coverage is indicated on the inner side of the arc, where solid segments indicate available experimentally determined structures and dashed outlines indicate homology models.

Sequence annotation features are displayed on mouse-over to the outer side of the arc, and include InterPro domains, PFAM domains, variants, transmembrane regions, disulphide bonds, nucleotide binding regions, signal peptides and active site residues. The same information is also provided by the Sequence Features pull-down menu.

In this view, structures and models are grouped based on coverage and oligomeric state. The available models for the entry are listed at the bottom of the page.


Entry summary

The entry summary provides general information about the target protein, including the name of the protein and links to related information in UniProtKB, InterPro and STRING databases.

For each selected model, the following information is provided: the PDB ID of the structure used as a template for modelling, the target-template sequence identity and similarity, the date of the last update of the model, the model quality estimate and a link for downloading the model coordinates.

Three different model quality plots are shown, providing an estimate of both global and local quality of the model as assessed by the QMEAN scoring function, thus allowing for the identification of unreliable or poorly modeled regions (or even residues) of a model.

The first two plots show the global and local model quality respectively, while the third plot shows the QMEAN Z-score of the model in comparison with experimental protein structures from the PDB. The latter plot gives an indication on how similar a given model is in terms of mean force potential to experimental structures of comparable size (further details are provided in the Model quality section below).

In case the user prefers to build a model using a different template structure than the one selected automatically, e.g. in a different conformation state or with a specific ligand, an “Interactive Modelling” button is provided with a link to the SWISS-MODEL workspace. Here the user can start a new interactive modelling session with the target sequence preloaded for initiating a new template selection.


3D structure visualization

This section provides an inpage visualization of the currently selected model/structure. The graphical view has been implemented using PV, an interactive JavaScript/WebGL based 3D structure viewer and NGL, a web application for molecular visualization. All sections in the SMR entry page are linked to the 3D structure viewer. Any selected feature from the entry summary or the sequence alignment can be visualized on the structure and vice versa (i.e. a residue selected in the structure is highlight in the alignment).

Buttons are provided below the 3D viewer allowing for some extra functionalities such as taking a snapshot or running PV in a separate window.


Target-template sequence alignment

Details regarding the alignment between the target and the template are provided. The configuration button allows applying various colouring schemes to the sequence and the 3D model shown in PV. Amongst others, the user can colour the alignment and the structure by amino acid properties, QMEAN score, as well as by chain or secondary structure. An option is also provided to export the alignment in any of the following formats: FASTA, Clustal and PNG.

Below the alignment, a table is provided where all available experimental structures and models are listed, allowing an in depth exploration of the available structure information for the entry.


Model quality

Each model in SMR is evaluated by QMEAN (Benkert et al.) to provide model quality measures on a per-residue basis as well as a global scale. The graphs provide plots of the estimated local quality of each part of the model as well as how the model compares to other structures in the PDB. In the main overview graph, colours are used to provide quality information at a glance with blue indicating good and red indicating bad quality scores for the specific feature. To relate the model quality to high resolution X-ray structures of similar size, QMEAN values are expressed as a Z-score.

Per-residue quality values are also provided in the B-factor column of the PDB file of the model.


On-demand update of individual entries

If no structure or model is available for a given UniProtKB entry, the user can request either an automated update of the SMR entry or start an interactive modelling job using the SWISS-MODEL Workspace by clicking the "Build Models" Button.

Please notice that it may take up to 15 minutes before a model is added to the Repository.
Please notice that models with low quality estimate are not added to the repository.


API

The new SWISS-MODEL Repository is continuously updated to provide the user with with the best available model/experimental structure for a given UniProtKB AC.

Due to this continuous update, there are no fixed URLs to specific versions of models, and indeed models may no longer exist if the best available template has been updated meanwhile.

To find out what is currently available in SMR, first get a list of available models and experimental structures in JSON format (here UniProtKB AC P07900 is used as an example).

  • https://swissmodel.expasy.org/repository/uniprot/P07900.json

    Returns a JSON formatted file with a list of homology models and experimental structures for UniProtKB entry P07900

  • https://swissmodel.expasy.org/repository/uniprot/P07900.json?provider=swissmodel

    Returns a JSON formatted file with either homology models (provider=swissmodel) or experimental structures (provider=pdb) for UniProtKB entry P07900

  • https://swissmodel.expasy.org/repository/uniprot/P07900.json?template=5fwp.1.B

    Returns a JSON formatted file with a list of homology models and experimental structures for the template 5fwp.1.B. The template id can be indicated in one of the following formats: 5fwp, 5fwpB, 5fwp.1.B

  • https://swissmodel.expasy.org/repository/uniprot/P07900.json?range=15-250

    Returns a JSON formatted file with a list of homology models and experimental structures that cover residues 15-250 of the target sequence

From the list of available models, the user can select a specific model or structure based on desired parameters or a combination of them, i.e. QMEAN, SeqId, range etc., and fetch the coordinates using the URL provided in the "coordinates" field.

As previously stated, the continuous update of SMR means a specific model may not exist anymore, so no specific model ID is available. However, for a given entry, the API will return the best model/structure available. The best model is the the one with the highest quality based on QMEAN. The “sort” parameter allows to sort the models by sequence identity or sequence similarity to template. Experimental structures can be sorted based on stoichiometry, range, experimental method and resolution. If no provider is specified, experimental structures will be returned before homology models.

An example of combined URL is the following:

https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?from=14&to=223&template=2k5b&provider=pdb

If no model is found for your requested coordinates, a 404 Not Found error will be raised.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb

    Returns the best homology model or experimental structure in PDB format.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?sort=seqid

    Returns the best homology model or experimental structure in PDB format sorted by sequence identity.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?sort=seqsim

    Returns the best homology model or experimental structure in PDB format sorted by sequence similarity.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?provider=swissmodel

    Returns the best homology model or experimental structure from the given provider in PDB format.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?template=5fwk.1.B

    Returns the best homology model or experimental structure based on the given template in PDB format.

  • https://swissmodel.expasy.org/repository/uniprot/P07900.pdb?range=15-250

    Returns the best homology model or experimental structure which overlaps the given range.