The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
The SWISS-MODEL Repository and associated resources
Open accessAbstract
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.
Overview
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Integrity signals
Registry
Cites
Statistics
Verification
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Self-check
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Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Zhou, H., & Zhou, Y. (2002) · Protein Science · doi:10.1110/ps.0217002 · Cited by 902 · cited 1×
“Therefore, entries from the Repository can be directly submitted to the Workspace for quality assessment using different global and local quality scores such as DFire ( 45 ), ProQRes (46) or QMEAN (47).”
MethodComputational design of antibody-affinity improvement beyond in vivo maturation
Lippow, S. M., Wittrup, K. D., & Tidor, B. (2007) · Nature Biotechnology · doi:10.1038/nbt1336 · Cited by 342
Integrating biological data – the Distributed Annotation System
Jenkinson, A. M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R. D., Hermjakob, H., Hubbard, T. J., Jimenez, R. C., Jones, P., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s8-s3 · Cited by 100 · cited 10×
“The SWISS-MODEL Repository DAS service is accessible at http://swissmod el.expasy.org/service/das/swissmodel/.”
BackgroundMethodInfluential
Cited by
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398
QMEAN server for protein model quality estimation
Benkert, P., Künzli, M., & Schwede, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp322 · Cited by 873
Self-citationPioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.017 · Cited by 780
A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains
Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.035 · Cited by 693
“, 2014) and, when necessary, SWISS-MODEL database (Kiefer et al., 2009), were calculated using the PISA software, as contained in version 6.”
MethodComparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
“This protocol should also include assessment using the best computational tools currently available, such as the model assessment methods covered in this text, and those cataloged at the Protein Model Portal ( http://proteinmodelportal.org ; Arnold et al., 2009; Haas et al., 2013).”
Method
Metadata
- Authors
- Kiefer, F., Arnold, K., Kunzli, M., Bordoli, L., & Schwede, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D387-D392
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2118200955
- Cited by
- 2,012
- References
- 4
- FWCI
- 34.37
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The SWISS-MODEL Repository and associated resources. https://app.cochat.ai/papers/10.1093/nar/gkn750
- The paper
- Kiefer, F., Arnold, K., Kunzli, M., Bordoli, L., & Schwede, T. (2009). The SWISS-MODEL Repository and associated resources. Nucleic Acids Research. https://doi.org/10.1093/nar/gkn750
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
