ArticleScientific reports2015
Dimeric interactions and complex formation using direct coevolutionary couplings.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Identification and engineering of highly functional potyviral proteases in cells using co-evolutionary models.Nature communications · 2026Article
- Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding.Nature communications · 2025Article
- Mapping the energy landscape of a fold-switching protein MAD2.Protein science : a publication of the Protein Society · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Engineering Proteins Using Statistical Models of Coevolutionary Sequence Information.Cold Spring Harbor perspectives in biology · 2024Review
- Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.Biophysical journal · 2024Article
- Latent generative landscapes as maps of functional diversity in protein sequence space.Nature communications · 2023Article
- Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits.Computational and structural biotechnology journal · 2023Article
- Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation.Biophysical journal · 2022Article
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.PLoS computational biology · 2022Article
- Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor.ACS synthetic biology · 2022Article
- Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein.Computational and structural biotechnology journal · 2022Review
- Divergence in Dimerization and Activity of Primate APOBEC3C.Journal of molecular biology · 2021Article
- Evolution of frustrated and stabilising contacts in reconstructed ancient proteins.European biophysics journal : EBJ · 2021Article
- Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction.International journal of molecular sciences · 2021Review
- On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction.NAR genomics and bioinformatics · 2021Article
- Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus.Biophysical journal · 2021Article
- Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential.The journal of physical chemistry. B · 2020Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.