ArticleJournal of structural biology2011
Modeling protein structure at near atomic resolutions with Gorgon.
Article in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- All-atom RNA structure determination from cryo-EM maps.Nature biotechnology · 2025Article
- Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.Nature communications · 2024Article
- Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg.ACS omega · 2024Article
- Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.Biophysical journal · 2024Review
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions.Current opinion in structural biology · 2023Review
- LPTD: a novel linear programming-based topology determination method for cryo-EM maps.Bioinformatics (Oxford, England) · 2022Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB discovery · 2022Article
- Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps.Biomolecules · 2021Article
- EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps.Briefings in bioinformatics · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction - A Case Study.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange.Progress in biophysics and molecular biology · 2019Article
- Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.Journal of structural biology · 2018Article
- CryoEM-based hybrid modeling approaches for structure determination.Current opinion in microbiology · 2018Review
- Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem.Molecules (Basel, Switzerland) · 2018Article
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Authors and funding
10 authors.
Funding
Abstract
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.
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