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Comparative Protein Structure Modeling Using MODELLER
Open accessAbstract
Comparative protein structure modeling predicts the three‐dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
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Xu, L., Jin, S., Urem, M., Lee, S.-J., Lamers, M. H., Chen, X., Wolynes, P. G., & Wuite, G. J. L. (2025) · Nature Communications · doi:10.1038/s41467-025-62531-1 · Cited by 3
AlphaMut: A Deep Reinforcement Learning Model to Suggest Helix-Disrupting Mutations
Bhargav, P., & Mukherjee, A. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01387 · Cited by 2
WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families
Brownless, A.-L. R., Harrison-Rawn, T., & Kamerlin, S. C. L. (2025) · JACS Au · doi:10.1021/jacsau.5c00447 · Cited by 2
Deguchi, T., Ab Ghani, N. S., Kurumida, Y., Iida, S., Kobayashi, K., & Saito, Y. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf536 · Cited by 2
Gu, C., Takada, S., Brandani, G. B., & Terakawa, T. (2025) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012493 · Cited by 1
Ketaren, N. E., Mast, F. D., Fridy, P. C., Olivier, J. P., Sanyal, T., Sali, A., Chait, B. T., Rout, M. P., & Aitchison, J. D. (2023) · doi:10.1101/2023.07.14.549041 · Cited by 1
Self-citationGiordano, D., d’Acierno, A., Marabotti, A., Iovino, P., Iacomino, G., & Facchiano, A. (2024) · Genes · doi:10.3390/genes15081073 · Cited by 1
Barron, M. P., Wijeratne, H. R. S., Runnebohm, A. M., Caric, K. M., Mosley, A. L., & Vilseck, J. Z. (2025) · doi:10.1101/2025.06.30.662390 · Cited by 1
The partitioning of fatty acids between membrane and storage lipids controls ER membrane expansion.
Lysyganicz, P. K., Barbosa, A. D., Khondker, S., Stewart, N. A., Carman, G. M., Stansfeld, P. J., Dymond, M. K., & Siniossoglou, S. (2024) · doi:10.1101/2024.09.05.611378 · Cited by 1
Yamauchi, M., Brandani, G. B., Terakawa, T., & Takada, S. (2026) · eLife · doi:10.7554/elife.106752
Metadata
- Authors
- Webb, B., & Sali, A.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2016-06
- Volume
- 54
- Issue
- 1
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W4211196614
- Cited by
- 4,316
- References
- 10
- FWCI
- 136.33
- Type
- journal article
- Language
- en
- Open access
- bronze
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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
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.
