ArticleBiopolymers2012
Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.
Article in Biopolymers, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.Biophysical journal · 2024Review
- The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.PLoS pathogens · 2023Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization.Biomimetics (Basel, Switzerland) · 2021Article
- Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins.Viruses · 2020Article
- Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.Nature communications · 2019Article
- De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.Journal of structural biology · 2018Article
- FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.Nucleic acids research · 2018Article
- A fragment based method for modeling of protein segments into cryo-EM density maps.BMC bioinformatics · 2017Article
- Article
- Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.Journal of chemical theory and computation · 2017Article
- Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.BioMed research international · 2017Article
- De Novo modeling in cryo-EM density maps with Pathwalking.Journal of structural biology · 2016Article
- Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.Biophysical journal · 2016Article
- 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.Biophysical journal · 2016Article
- Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.Methods in enzymology · 2016Review
- Article
- Numerical geometry of map and model assessment.Journal of structural biology · 2015Article
- Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.Nature methods · 2015Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
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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.