Mapping Monomeric Threading to Protein–Protein Structure Prediction
Open accessAbstract
The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD <2.5 Å by SPRING is 134% and 167% higher than these competing methods. SPRING is controlled with ZDOCK on 77 docking benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.
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The whole-proteome SPRING threading search predicts a sparse interactome, with 2.6% (2483) of 95,703 protein pairs identified as PPI partners.
“The interactome predicted by whole-proteome SPRING threading search is relatively sparse, with only 2.6% (2483) of all 95,703 protein pairs being predicted PPI partners (Figure 4A).”
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- Authors
- Guerler, A., Govindarajoo, B., & Zhang, Y.
- Affiliations
- University of Michigan (US)
- Corresponding author
- Zhang, Yang
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-02-27
- Volume
- 53
- Issue
- 3
- Pages
- 717-725
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC4076494
- OpenAlex
- W2142895465
- Cited by
- 73
- References
- 37
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 3 · 2023: 3 · 2022: 7 · 2021: 11 · 2020: 3 · 2019: 8 · 2018: 5 · 2017: 2 · 2016: 10 · 2015: 8 · 2014: 6 · 2013: 1
- FWCI
- 3.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (GM-083107, R01GM084222, R25GM086262, GM-084222, R01GM083107)
- 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
- template-based structure prediction, protein complexes, springs, protein-protein interaction, protein docking, ZDOCK
- MeSH terms
- Algorithms, Models, Molecular, Protein Conformation, Proteins, Software, Sequence Alignment, Dimerization, Benchmarking, Databases, Protein
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