ArticleNucleic acids research2006
Protein complex compositions predicted by structural similarity.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A knowledge-based scoring function to assess quaternary associations of proteins.Bioinformatics (Oxford, England) · 2020Article
- Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions.Nucleic acids research · 2019Article
- Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data.Scientific reports · 2018Article
- Non-interacting proteins may resemble interacting proteins: prevalence and implications.Scientific reports · 2017Article
- HOMCOS: an updated server to search and model complex 3D structures.Journal of structural and functional genomics · 2016Article
- Multiplex matrix network analysis of protein complexes in the human TCR signalosome.Science signaling · 2016Article
- Computational approaches for prediction of pathogen-host protein-protein interactions.Frontiers in microbiology · 2015Review
- Structure homology and interaction redundancy for discovering virus-host protein interactions.EMBO reports · 2013Article
- Toward a "structural BLAST": using structural relationships to infer function.Protein science : a publication of the Protein Society · 2013Review
- Article
- SALIGN: a web server for alignment of multiple protein sequences and structures.Bioinformatics (Oxford, England) · 2012Article
- Expanding the conformational selection paradigm in protein-ligand docking.Methods in molecular biology (Clifton, N.J.) · 2012Article
- The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold.BMC evolutionary biology · 2011Article
- On the role of electrostatics in protein-protein interactions.Physical biology · 2011Review
- Mapping protein interactions between Dengue virus and its human and insect hosts.PLoS neglected tropical diseases · 2011Article
- ModBase, a database of annotated comparative protein structure models, and associated resources.Nucleic acids research · 2011Article
- Integrative structure modeling of macromolecular assemblies from proteomics data.Molecular & cellular proteomics : MCP · 2010Article
- PCFamily: a web server for searching homologous protein complexes.Nucleic acids research · 2010Article
- Protein interface conservation across structure space.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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6 authors.
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Abstract
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (http://salilab.org/pibase). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain-porcine alpha-amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (http://salilab.org/modbase).
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