The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Templates are available to model nearly all complexes of structurally characterized proteins
Open accessAbstract
Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides the possibility of aligning the structures of the proteins and the template complexes. The progress in the development of template-based docking and the vast experience in template-based modeling of individual proteins show that, generally, such approaches are more reliable than the free modeling. The key aspect of this modeling paradigm is the availability of the templates. The current common perception is that due to the difficulties in experimental structure determination of protein-protein complexes, the pool of docking templates is insignificant, and thus a broad application of template-based docking is possible only at some future time. The results of our large scale, systematic study show that, surprisingly, in spite of the limited number of protein-protein complexes in the Protein Data Bank, docking templates can be found for complexes representing almost all the known protein-protein interactions, provided the components themselves have a known structure or can be homology-built. About one-third of the templates are of good quality when they are compared to experimental structures in test sets extracted from the Protein Data Bank and would be useful starting points in modeling the complexes. This finding dramatically expands our ability to model protein interactions, and has far-reaching implications for the protein docking field in general.
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“The rise of the comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine [12,13].”
From Challenges in protein docking (2020) · cites this paper as [12]
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
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
TM-align: a protein structure alignment algorithm based on the TM-score
Zhang, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki524 · Cited by 3,774
The Database of Interacting Proteins: 2004 update
Salwinski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh086 · Cited by 2,271
An improved algorithm for matching biological sequences
Gotoh, O. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90398-9 · Cited by 1,726
PIPER: An FFT‐based protein docking program with pairwise potentials
Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21117 · Cited by 865
CAPRI: A Critical Assessment of PRedicted Interactions
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703
Critical assessment of methods of protein structure prediction (CASP) — round x
Moult, J., Fidelis, K. A., Kryshtafovych, A., Schwede, T. F., & Tramontano, A. L. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24452 · Cited by 687
The Biomolecular Interaction Network Database and related tools 2005 update
Alfarano, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki051 · Cited by 587
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V. L., Wassenaar, T. A., & Bonvin, A. M. J. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21723 · Cited by 555
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Tandon, H., Vattekatte, A. M., Srinivasan, N., & Sandhya, S. (2020) · Toxins · doi:10.3390/toxins12080481 · Cited by 13
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Han, Y., Cheng, L., & Sun, W. (2019) · Protein and Peptide Letters · doi:10.2174/0929866526666191105142034 · Cited by 10
Li, H., Yang, S., Wang, C., Zhou, Y., & Zhang, Z. (2016) · Plant Molecular Biology · doi:10.1007/s11103-016-0498-z · Cited by 10
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Balci, A. T., Gümeli, C., Hakouz, A., Yüret, D., Keskin, Ö., & Gürsoy, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/617506 · Cited by 9
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Igarashi, M., Hirokawa, T., Takadate, Y., & Takada, A. (2021) · Viruses · doi:10.3390/v13050913 · Cited by 9
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Preto, A. J., de Almeida, J. G., Schaarschmidt, J., Xue, L. C., Moreira, I. S., & Bonvin, A. M. J. J. (2018) · Wiley eBooks · doi:10.1002/9780470027318.a9615 · Cited by 1
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Ying, Y. M., Sang, M., Au, G., Chhibber, S., Du, Y., Fischer, J., Foley, S. L., Guo, S., Herzog-Pohl, I., Liu, Z. H., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.702082
Structural prediction of protein assemblies with deep learning
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Metadata
- Authors
- Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A.
- Affiliations
- University of Kansas (US)
- University of California San Diego (US)
- Université Paris-Sud (FR)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-05-29
- Volume
- 109
- Issue
- 24
- Pages
- 9438-9441
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3386081
- OpenAlex
- W2163614321
- Cited by
- 179
- References
- 34
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 3 · 2023: 7 · 2022: 16 · 2021: 11 · 2020: 18 · 2019: 14 · 2018: 12 · 2017: 16 · 2016: 22 · 2015: 9 · 2014: 18 · 2013: 20 · 2012: 3
- FWCI
- 6.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM074255)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- template-based docking, protein-protein docking, protein-protein complex, Protein Data Bank, protein-protein interaction, homology modeling, structural alignment
- MeSH terms
- Models, Molecular, Proteins, Databases, Protein
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