The SWISS-MODEL Repository—new features and functionality

By Stefan Bienert, Andrew M. Waterhouse, Tjaart A. P. de Beer, Gerardo Tauriello, Gabriel Studer, Lorenza Bordoli, Torsten Schwede. 2016

1,525 citations recorded by the source corpus.

SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline. It currently holds >400 000 high quality models covering almost 20% of Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update of features and functionalities which have been implemented recently. We address improvements in target coverage, model quality estimates, functional annotations and improved in-page visualization. We also introduce a new update concept which includes regular updates of an expanded set of core organism models and UniProtKB-based targets, complemented by user-driven on-demand update of individual models. With the new release of the modeling pipeline, SMR has implemented a REST-API and adopted an open licencing model for accessing model coordinates, thus enabling bulk download for groups of targets fostering re-use of models in other contexts. SMR can be accessed at https://swissmodel.expasy.org/repository.

Subfields: Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “The SWISS-MODEL Repository (39) (SMR, https:// swissmodel.expasy.org/repository) is a database of automatically generated homology models for relevant model organisms and experimental structure information for all sequences in UniProtKB (34).”
A structural inventory of native ribosomal ABCE1‐43S pre‐initiation complexes (2020, positive): “Homology models were created using SWISS-MODEL Repository (Bienert et al , 2017; Waterhouse et al , 2018).”
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina (2024, background): “SwissDock 2024 also provides an advanced target search option in three different structural databases: PDBe ( 26 ), SWISS-MODEL ( 29 ), and the AlphaFold protein structure database ( 28 ,37 ).”
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism (2019, methodology): “High quality 3D protein structures at genome scale are still scarce 53 , thus the breakthrough in 3D proteins structure simulations 55 and the related residues functional predictions are strongly expected.”
A structural biology community assessment of AlphaFold2 applications (2021, methodology): “Regarding coverage, previous attempts to generate ‘proteome-wide’ structural models include those based on homology models, such as the SWISS-MODEL Repository (SMR) 14 , and more recently, the modeling of known protein domains in the Pfam database 15 using trRosetta 16 .”