The SWISS-MODEL Repository 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 for all sequences in Swiss-Prot and relevant model organisms. The database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. The repository allows users to assess model quality, search for alternative template structures, and build models interactively via the SWISS-MODEL Workspace. Annotation with functional information and cross-linking with other databases, such as the Protein Model Portal, facilitates navigation between protein sequence and structure resources. The repository contains models generated by a fully automated homology modelling pipeline. Homology modelling involves selecting a suitable template, aligning the target sequence with the template structure, building the model, energy minimization, and model quality assessment. The SWISS-MODEL pipeline integrates these steps into a fully automated workflow. A hierarchical template search and selection protocol is implemented to ensure efficient and accurate template selection. Templates are ranked based on E-value, sequence identity, resolution, and structure quality. The best templates are selected to maximize the length of the modelled region of the protein. The SWISS-MODEL Repository is a relational database of models generated by the automated SWISS-MODEL pipeline based on protein sequences from the UniProt database. Model target sequences are uniquely identified by their md5 cryptographic hash of the full length raw amino acid sequence. This allows for the reduction of redundancy in protein sequence databases and facilitates cross-referencing with databases using different accession code systems. The repository is updated regularly to include new target sequences and take advantage of newly available template structures. The current release contains 3.45 million models for 2.72 million unique sequences, built on 26,185 different template structures, covering 48.8% of the entries from UniProt (14.0) and 65.4% of the unique sequences of Swiss-Prot. The web interface provides the main entry point to the SWISS-MODEL Repository. Models for specific proteins can be queried using different database accession codes or directly with the protein amino acid sequence. A graphical overview of the segments for which models are available is shown. Functional and domain annotation is retrieved dynamically using web service protocols. The md5-based reference frame allows for updating the database accession mappings between modelling release cycles. The SWISS-MODEL Repository is integrated with the SWISS-MODEL Workspace, which provides an interactive web-based environment for protein structure homology modelling. The repository is also integrated with the Protein Model Portal, allowing cross-linking with other resources. The repository provides programmatic access via DAS (distributed annotation system) and allows for seamless integration with other resources. The SWISS-MODEL Repository is a large-scale database of pre-computed 3DThe SWISS-MODEL Repository 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 for all sequences in Swiss-Prot and relevant model organisms. The database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. The repository allows users to assess model quality, search for alternative template structures, and build models interactively via the SWISS-MODEL Workspace. Annotation with functional information and cross-linking with other databases, such as the Protein Model Portal, facilitates navigation between protein sequence and structure resources. The repository contains models generated by a fully automated homology modelling pipeline. Homology modelling involves selecting a suitable template, aligning the target sequence with the template structure, building the model, energy minimization, and model quality assessment. The SWISS-MODEL pipeline integrates these steps into a fully automated workflow. A hierarchical template search and selection protocol is implemented to ensure efficient and accurate template selection. Templates are ranked based on E-value, sequence identity, resolution, and structure quality. The best templates are selected to maximize the length of the modelled region of the protein. The SWISS-MODEL Repository is a relational database of models generated by the automated SWISS-MODEL pipeline based on protein sequences from the UniProt database. Model target sequences are uniquely identified by their md5 cryptographic hash of the full length raw amino acid sequence. This allows for the reduction of redundancy in protein sequence databases and facilitates cross-referencing with databases using different accession code systems. The repository is updated regularly to include new target sequences and take advantage of newly available template structures. The current release contains 3.45 million models for 2.72 million unique sequences, built on 26,185 different template structures, covering 48.8% of the entries from UniProt (14.0) and 65.4% of the unique sequences of Swiss-Prot. The web interface provides the main entry point to the SWISS-MODEL Repository. Models for specific proteins can be queried using different database accession codes or directly with the protein amino acid sequence. A graphical overview of the segments for which models are available is shown. Functional and domain annotation is retrieved dynamically using web service protocols. The md5-based reference frame allows for updating the database accession mappings between modelling release cycles. The SWISS-MODEL Repository is integrated with the SWISS-MODEL Workspace, which provides an interactive web-based environment for protein structure homology modelling. The repository is also integrated with the Protein Model Portal, allowing cross-linking with other resources. The repository provides programmatic access via DAS (distributed annotation system) and allows for seamless integration with other resources. The SWISS-MODEL Repository is a large-scale database of pre-computed 3D