How to make contact maps of protein trajectory?
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Protein contact maps can be constructed from protein trajectories using various approaches outlined in the provided research contexts. One method involves utilizing a directed walk strategy in the residue-level contact-map space to generate protein folding trajectories, enabling the characterization of folding pathways . Another technique involves using a generative adversarial neural network embedded with modified squeeze and excitation residual networks to predict contact maps accurately, especially for proteins lacking homologous templates . Additionally, a novel deep neural network framework combining ResNet and DenseNet has been proposed for contact prediction, incorporating features like position-specific frequency matrix to enhance prediction accuracy . These methods offer valuable insights into constructing contact maps from protein trajectories, aiding in understanding protein dynamics and interactions.
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| Papers (4) | Insight |
|---|---|
| Contact maps of protein trajectories can be made using MDcons, which analyzes inter-residue contacts at the interface to assess similarity between snapshots, aiding in understanding complex dynamics. | |
| Not addressed in the paper. | |
| Contact maps of protein trajectory can be made using a protein-ligand contact fingerprint (cF P) built with a specific algorithm, focusing on early and late unbinding stages using MD Traj and contactmap libraries. | |
| Contact maps of protein trajectories can be made using a directed walk strategy in the residue-level contact-map space, facilitating protein-folding pathway generation without traditional challenges like long time scales. |
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