The SWISS-MODEL Repository and associated resources

By Florian Kiefer, Konstantin Arnold, Michael Künzli, Lorenza Bordoli, Torsten Schwede. 2008

2,130 citations recorded by the source corpus.

SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide 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 models organisms. 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 are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-MODEL Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace (http://swissmodel.expasy.org/workspace/). Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Torsten Schwede
2. Ben M. Webb
3. Andrej Sali
4. Yang Zhang
5. Andriy Kryshtafovych
6. Krzysztof Fidelis
7. Gaetano T. Montelione
8. John Moult

In Molecular Biology

1. Torsten Schwede
2. Andrej Sali
3. Ben M. Webb
4. Yang Zhang
5. Andriy Kryshtafovych
6. Jinbo Xu
7. Burkhard Rost
8. David Baker

Citations in the corpus

• The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
• Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, methodology): “The Protein Model Portal (Arnold et al., 2008) in particular provides access to models calculated by SWISS-MODEL (Kiefer et al., 2009) and ModBase (Pieper et al., 2009), as well as models produced by the four PSI large-scale production centers (http://www.proteinmodelportal.org/).”
• The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, methodology): “PMP relies on models provided by several research groups such as Center for Structures of Proteins in Membranes (CSMP) (12), North Eastern Structural Genomics Center (NESG) (13), New York Structural Genomics Research Consortium (NYSGRC) (14), ModBase (15), SWISS-MODEL Repository (16) and GPCRDB (17)”
• Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, methodology): “Three models have been built for the MNDA protein by three resources accessible trough the portal: ModBase (55), Swiss-Model Repository (36), and NESG (104).”
• QMEAN server for protein model quality estimation (2009, methodology): “Models from the SWISS-MODEL Repository (31) can be directly sent to the quality estimation section of the Workspace.”
• The Protein Model Portal (2008, neutral): “The current release of the portal allows searching 7.6 million model structures provided by the different partner sites: CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase [32], SWISS-MODEL Repository [33].”
• Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, neutral): “…(Raman et al., 2009) Rosetta https://www.rosettacommons.org (Das and Baker, 2008) SWISS-MODEL Repository http://swissmodel.expasy.org/repository (Kiefer et al., 2009) SWISS-MODEL Workspace http://swissmodel.expasy.org/workspace/ (Arnold et al., 2006; Bordoli and Schwede, 2012) Structure.”
• FreeContact: fast and free software for protein contact prediction from residue co-evolution (2014, background): “Homology modeling [4] or comparative modeling [5] is the only bridge that allows reliable modeling of 3D structure for about 20-40% of the residues in all known proteins [6].”
• An estimated 5% of new protein structures solved today represent a new Pfam family (2013, background): “This technique allows us to computationally predict the three-dimensional coordinates of a previously structurally uncharacterized protein using information from the experimental structure of one or more of its homologues (Kiefer et al., 2009; Pieper et al., 2004).”
• STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “Each protein node in the network shows a preview to 3D structural information, if available, and can be clicked to reveal a pop-up window with more information about the protein [including its annotation (58), SMART domain-structure (59), structure homology models from SWISS-MODEL Repository (60), e”
• Computational Methods in Drug Discovery (2014, methodology): “SWISS-MODEL repository contains annotated 3D protein models generated by homology modeling of all sequences in SWISS-PROT (Kiefer et al., 2009).”