ArticleJournal of structural biology2013
Computational methods for constructing protein structure models from 3D electron microscopy maps.
Article in Journal of structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Protein Secondary Structure and DNA/RNA Detection for Cryo-EM and Cryo-ET Using Emap2sec and Emap2secMethods in molecular biology (Clifton, N.J.) · 2025Article
- Secondary Structure Detection and Structure Modeling for Cryo-EM.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Artificial Intelligence in Cryo-Electron Microscopy.Life (Basel, Switzerland) · 2022Review
- Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Current protocols · 2022Article
- MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Frontiers in molecular biosciences · 2022Article
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
- MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.Journal of chemical information and modeling · 2020Article
- Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length.Frontiers in molecular biosciences · 2020Article
- Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal · 2020Review
- De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.Journal of structural biology · 2018Article
- De novo main-chain modeling for EM maps using MAINMAST.Nature communications · 2018Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Variability of Protein Structure Models from Electron Microscopy.Structure (London, England : 1993) · 2017Article
- Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps.Frontiers in molecular biosciences · 2017Article
- De Novo modeling in cryo-EM density maps with Pathwalking.Journal of structural biology · 2016Article
- γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm.Structure (London, England : 1993) · 2015Article
- Article
- Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.Journal of chemical theory and computation · 2015Article
- Collective variable approaches for single molecule flexible fitting and enhanced sampling.Chemical reviews · 2014Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.
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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.