ArticleProteins2010
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Artificial Intelligence in Cryo-Electron Microscopy.Life (Basel, Switzerland) · 2022Review
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Mapping the native organization of the yeast nuclear pore complex using nuclear radial intensity measurements.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Archiving and disseminating integrative structure models.Journal of biomolecular NMR · 2019Article
- Review
- Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.Journal of molecular biology · 2018Article
- Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Integrative structure modeling with the Integrative Modeling Platform.Protein science : a publication of the Protein Society · 2018Article
- Article
- Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies.Scientific reports · 2017Article
- Performance of ZDOCK and IRAD in CAPRI rounds 28-34.Proteins · 2017Article
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.Acta crystallographica. Section D, Structural biology · 2016Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology.Journal of the American Society for Mass Spectrometry · 2016Review
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.Biophysical journal · 2016Article
- 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.Biophysical journal · 2016Article
- γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm.Structure (London, England : 1993) · 2015Article
- Article
- An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.BMC bioinformatics · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
Structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. Determining these structures is a major challenge for experimental techniques, such as X-ray crystallography, NMR spectroscopy and electron microscopy (EM). Thus, computational modeling techniques, including molecular docking, are required. The development of most molecular docking methods has so far been focused on modeling of binary complexes. We have recently introduced the MultiFit method for modeling the structure of a multisubunit complex by simultaneously optimizing the fit of the model into an EM density map of the entire complex and the shape complementarity between interacting subunits. Here, we report algorithmic advances of the MultiFit method that result in an efficient and accurate assembly of the input subunits into their density map. The successful predictions and the increasing number of complexes being characterized by EM suggests that the CAPRI challenge could be extended to include docking-based modeling of macromolecular assemblies guided by EM.
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