Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps
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Summary
This work developed a method to predict the topology and sequence alignment for the skeleton helices of protein complexes using the Rosetta ab initio structure prediction method, and analyzed the use of the skeletons as a clustering tool for the decoy structures generated by Rosetta.
- Type
- article
- Published
- 2008-02-01
- Cited by
- 20
- References
- 26
- OpenAlex
- https://openalex.org/W18324752
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:21493355
Keywords
Economic growth, Geography, Political science, Development economics, Economics
References
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Cited by
- Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph
- Parallel Computing in Protein Structure Topology Determination
- Persistent topology for cryo‐EM data analysis
- Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data
- Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies
- Solving the Secondary Structure Matching Problem in Cryo-EM De Novo Modeling Using a Constrained K-Shortest Path Graph Algorithm
- Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions
- A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors
- Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
- Structure prediction for the helical skeletons detected from the low resolution protein density map
- An approximate robotics algorithm to assemble a loop between two helices
- Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem
- De novo protein structure modeling from cryoem data through a dynamic programming algorithm in the secondary structure topology graph
- Computational development for secondary structure detection from three-dimensional images of cryo-electron microscopy
- An efficient method for validating protein models using electron microscopy data
- PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models
- Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem
- Protein Loop Length Estimation From Medium Resolution Cryoem Images
- Towards De Novo Folding of Protein Structures from Cryo-EM 3 D Images at Medium Resolutions