Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Cryo-electron microscopy (2)
- Image (2)
- Secondary structure (2)
- 3-dimensional (1)
- 3D (1)
-
- Amino acid (1)
- Constraints (1)
- Contact (1)
- Convolutional (1)
- Deep learning (1)
- Index Medicus (1)
- MI (1)
- Molecular dynamics analysis (1)
- Mutual information (1)
- Neural networks (1)
- Protein (1)
- Protein design and engineering (1)
- Protein structure (1)
- Protien unfolding pathway (1)
- SMD (1)
- Steered molecular dynamics (1)
- Topology (1)
- Publication
- Publication Type
Articles 1 - 4 of 4
Full-Text Articles in Medicine and Health Sciences
Combine Cryo-Em Density Map And Residue Contact For Protein Structure Prediction: A Case Study, Maytha Alshammari, Jing He
Combine Cryo-Em Density Map And Residue Contact For Protein Structure Prediction: A Case Study, Maytha Alshammari, Jing He
College of Sciences Posters
Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments in 1D and a set of traces of secondary structures in 3D. In order to enhance the accuracy in ranking secondary structure topologies, we propose a method that combines three sources of information …
A Tool For Segmentation Of Secondary Structures In 3d Cryo-Em Density Map Components Using Deep Convolutional Neural Networks, Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
A Tool For Segmentation Of Secondary Structures In 3d Cryo-Em Density Map Components Using Deep Convolutional Neural Networks, Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
Computer Science Faculty Publications
Although cryo-electron microscopy (cryo-EM) has been successfully used to derive atomic structures for many proteins, it is still challenging to derive atomic structures when the resolution of cryo-EM density maps is in the medium resolution range, such as 5–10 Å. Detection of protein secondary structures, such as helices and β-sheets, from cryo-EM density maps provides constraints for deriving atomic structures from such maps. As more deep learning methodologies are being developed for solving various molecular problems, effective tools are needed for users to access them. We have developed an effective software bundle, DeepSSETracer, for the detection of protein secondary structure …
Mechanism For The Unfolding Of The Top7 Protein In Steered Molecular Dynamics Simulations As Revealed By Mutual Information Analysis, Ognjen Perišić, Willy Wriggers
Mechanism For The Unfolding Of The Top7 Protein In Steered Molecular Dynamics Simulations As Revealed By Mutual Information Analysis, Ognjen Perišić, Willy Wriggers
Mechanical & Aerospace Engineering Faculty Publications
We employed mutual information (MI) analysis to detect motions affecting the mechanical resistance of the human-engineered protein Top7. The results are based on the MI analysis of pair contact correlations measured in steered molecular dynamics (SMD) trajectories and their statistical dependence on global unfolding. This study is the first application of the MI analysis to SMD forced unfolding, and we furnish specific SMD recommendations for the utility of parameters and options in the TimeScapes package. The MI analysis provided a global overview of the effect of perturbation on the stability of the protein. We also employed a more conventional trajectory …
Combining Cryo-Em Density Map And Residue Contact For Protein Secondary Structure Topologies, Maytha Alshammari, Jing He
Combining Cryo-Em Density Map And Residue Contact For Protein Secondary Structure Topologies, Maytha Alshammari, Jing He
Computer Science Faculty Publications
Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set …