ArticlePloS one2012
ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Artificial molecular machines: Design and observation.Smart molecules : open access · 2023Review
- Integrative structural modeling of macromolecular complexes using Assembline.Nature protocols · 2022Review
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.Frontiers in molecular biosciences · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Frontiers in CryoEM Modeling.Journal of chemical information and modeling · 2019Article
- Review
- Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.Structure (London, England : 1993) · 2019Article
- Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.BMC structural biology · 2018Article
- CryoEM-based hybrid modeling approaches for structure determination.Current opinion in microbiology · 2018Review
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.Acta crystallographica. Section D, Structural biology · 2016Article
- 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
- Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.Molecules (Basel, Switzerland) · 2015Review
- A web interface for easy flexible protein-protein docking with ATTRACT.Biophysical journal · 2015Article
- Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa.Frontiers in microbiology · 2015Review
- A novel bio-sensor based on DNA strand displacement.PloS one · 2014Article
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Authors and funding
2 authors.
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Abstract
Many of the most important functions in the cell are carried out by proteins organized in large molecular machines. Cryo-electron microscopy (cryo-EM) is increasingly being used to obtain low resolution density maps of these large assemblies. A new method, ATTRACT-EM, for the computational assembly of molecular assemblies from their components has been developed. Based on concepts from the protein-protein docking field, it utilizes cryo-EM density maps to assemble molecular subunits at near atomic detail, starting from millions of initial subunit configurations. The search efficiency was further enhanced by recombining partial solutions, the inclusion of symmetry information, and refinement using a molecular force field. The approach was tested on the GroES-GroEL system, using an experimental cryo-EM map at 23.5 Å resolution, and on several smaller complexes. Inclusion of experimental information on the symmetry of the systems and the application of a new gradient vector matching algorithm allowed the efficient identification of docked assemblies in close agreement with experiment. Application to the GroES-GroEL complex resulted in a top ranked model with a deviation of 4.6 Å (and a 2.8 Å model within the top 10) from the GroES-GroEL crystal structure, a significant improvement over existing methods.
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