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stepdasha/spike
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This program calculates the distribution of the requested distance between any two atoms across all SARS-CoV-2 spike structures available in the Protein Data Bank.

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The SARS-CoV-2 Spike PDB Distance Tool is designed to analyze the distances between specific atoms across various structures of the SARS-CoV-2 spike protein available in the Protein Data Bank (PDB). Users can input the IDs and names of two residues, along with their corresponding atoms, to calculate the distance between them. Additionally, users can specify whether the residues are on the same chain or different chains. The tool also allows users to search for structures with specific mutations by providing the mutation's amino acid ID and name. Once the parameters are set, the tool generates a histogram displaying the distribution of distances across the selected structures. This tool offers a streamlined interface for exploring spatial relationships within the SARS-CoV-2 spike protein.

See owner's GitHub repository for more information: https://github.com/stepdasha/spike.

This app is based on the paper:

Stepanenko, D., Budhan, S., & Simmerling, C. (2023). SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. Journal of chemical information and modeling, 63(4), 1087–1092. https://doi.org/10.1021/acs.jcim.2c01366

This application was not uploaded by the author, but through their publicly available Github repository, https://github.com/stepdasha/spike.

Prototype

Warning: Not intended for clinical use. Assume outputs are unsafe and unvalidated. Use carefully.


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