ArticleStructure (London, England : 1993)2019
Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes.
Article in Structure (London, England : 1993), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Investigations on genomic, topological and structural properties of diguanylate cyclases involved inCurrent research in structural biology · 2025Article
- Multiple allostery in the regulation of PDGFR beta kinase activities.Acta biochimica et biophysica Sinica · 2024Article
- Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking.Nature communications · 2023Article
- Article
- Article
- Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches.International journal of molecular sciences · 2021Review
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry.ACS omega · 2019Article
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3 authors.
Funding
Abstract
Symmetrical homomeric proteins are ubiquitous in every domain of life, and information about their structure is essential to decipher function. The size of these complexes often makes them intractable to high-resolution structure determination experiments. Computational docking algorithms offer a promising alternative for modeling large complexes with arbitrary symmetry. Accuracy of existing algorithms, however, is limited by backbone inaccuracies when using homology-modeled monomers. Here, we present Rosetta SymDock2 with a broad search of symmetrical conformational space using a six-dimensional coarse-grained score function followed by an all-atom flexible-backbone refinement, which we demonstrate to be essential for physically realistic modeling of tightly packed complexes. In global docking of a benchmark set of complexes of different point symmetries-starting from homology-modeled monomers-we successfully dock (defined as predicting three near-native structures in the five top-scoring models) 17 out of 31 cyclic complexes and 3 out of 12 dihedral complexes.
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