Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone
Open accessAbstract
The structural modeling of protein interactions in the absence of close homologous templates is a challenging task. Recently, template-based docking methods have emerged to exploit local structural similarities to help ab-initio protocols provide reliable 3D models for protein interactions. In this work, we critically assess the performance of template-based docking in the twilight zone. Our results show that, while it is possible to find templates for nearly all known interactions, the quality of the obtained models is rather limited. We can increase the precision of the models at expenses of coverage, but it drastically reduces the potential applicability of the method, as illustrated by the whole-interactome modeling of nine organisms. Template-based docking is likely to play an important role in the structural characterization of the interaction space, but we still need to improve the repertoire of structural templates onto which we can reliably model protein complexes.
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Widely used and computationally efficient template-based docking methods are probably not applicable in TPD, since aid from structural alignment to known homologues may not be available.
“Moreover, widely used and computationally efficient template-based docking methods are probably not applicable in TPD, since aid from structural alignment to known homologues may not be available.241”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [241]
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Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
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- Authors
- Negroni, J., Mosca, R., & Aloy, P.
- Affiliations
- Institute for Research in Biomedicine (ES)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Corresponding author
- Aloy, Patrick
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2014-09
- Volume
- 22
- Issue
- 9
- Pages
- 1356-1362
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2083898222
- Cited by
- 35
- References
- 36
- Citations by year
- 2026: 1 · 2025: 1 · 2023: 2 · 2022: 1 · 2021: 3 · 2020: 5 · 2019: 4 · 2018: 1 · 2017: 8 · 2016: 6 · 2015: 2 · 2014: 1
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Structure (publishedVersion)
- PubMed (publishedVersion)
- Funders
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein interaction, protein complex structure prediction, structural templates, homology modeling, structural similarity
- MeSH terms
- Protein Binding, Proteins, Software, Protein Structure, Secondary, Protein Structure, Quaternary, Databases, Protein, Protein Interaction Domains and Motifs, Molecular Docking Simulation
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