ArticleStructure (London, England : 1993)2015
γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm.
Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed.
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
- Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Current protocols · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Integrative structural modeling of macromolecular complexes using Assembline.Nature protocols · 2022Review
- MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Frontiers in molecular biosciences · 2022Article
- Assessment of protein-protein interfaces in cryo-EM derived assemblies.Nature communications · 2021Article
- TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows.Acta crystallographica. Section D, Structural biology · 2021Article
- Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.Structure (London, England : 1993) · 2019Article
- Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry.Structure (London, England : 1993) · 2018Article
- Integrative modelling of cellular assemblies.Current opinion in structural biology · 2017Review
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We have developed a genetic algorithm for building macromolecular complexes using only a 3D-electron microscopy density map and the atomic structures of the relevant components. For efficient sampling the method uses map feature points calculated by vector quantization. The fitness function combines a mutual information score that quantifies the goodness of fit with a penalty score that helps to avoid clashes between components. Testing the method on ten assemblies (containing 3-8 protein components) and simulated density maps at 10, 15, and 20 Å resolution resulted in identification of the correct topology in 90%, 70%, and 60% of the cases, respectively. We further tested it on four assemblies with experimental maps at 7.2-23.5 Å resolution, showing the ability of the method to identify the correct topology in all cases. We have also demonstrated the importance of the map feature-point quality on assembly fitting in the lack of additional experimental information.
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Registered trials
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.