ArticleRobotica2016
Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem.
Article in Robotica, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A Novel Machine-Learning Based Method for Resolving Secondary Structure Topology in Medium-Resolution Cryo-EM Density Maps.International journal of molecular sciences · 2026Article
- Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements fromBiomolecules · 2023Article
- LPTD: a novel linear programming-based topology determination method for cryo-EM maps.Bioinformatics (Oxford, England) · 2022Article
- Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem.Molecules (Basel, Switzerland) · 2018Article
- An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map.Molecular based mathematical biology · 2017Article
- Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.BioMed research international · 2017Article
- Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem.Robotica · 2016Article
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2 authors.
Funding
Abstract
The cyclic coordinate descent (CCD) method is a popular loop closure method in protein structure modeling. It is a robotics algorithm originally developed for inverse kinematic applications. We demonstrate an effective method of building the backbone of protein structure models using the principle of CCD and a guiding trace. For medium-resolution 3-dimensional (3D) images derived using cryo-electron microscopy (cryo-EM), it is possible to obtain guiding traces of secondary structures and their skeleton connections. Our new method, constrained cyclic coordinate descent (CCCD), builds α-helices, β-strands, and loops quickly and fairly accurately along predefined traces. We show that it is possible to build the entire backbone of a protein fairly accurately when the guiding traces are accurate. In a test of 10 proteins, the models constructed using CCCD show an average of 3.91Å of backbone root mean square deviation (RMSD). When the CCCD method is incorporated in a simulated annealing framework to sample possible shift, translation, and rotation freedom, the models built with the true topology were ranked high on the list, with an average backbone RMSD100 of 3.76Å. CCCD is an effective method for modeling atomic structures after secondary structure traces and skeletons are extracted from 3D cryo-EM images.
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