Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
WolframChemistry/
Protein
Functions for protein visualizations
Contributed by: Soutick Saha, Wolfram Alpha
Explore the fascinating world of biomolecular structure with our state-of-the-art Wolfram paclet! Designed for researchers, educators, and structural biology enthusiasts alike, this powerful tool offers an immersive experience for visualizing the intricate structures of biomolecules, including proteins, nucleic acids, and their complexes. Explore the elegant geometry of molecular backbones, amide planes, and more with captivating 3D graphics. Delve deeper into the world of structural biology by computing and visualizing key features such as contact maps and dihedral angles. Whether you are analyzing protein structures, studying nucleic acid interactions, or simply marveling at the beauty of nature's molecular machines, our paclet empowers you to visualize biomolecules in a new light. Experience the wonder of biomolecular visualization—get started with our paclet today!
Installation Instructions
To install this paclet in your Wolfram Language environment,
evaluate this code:
PacletInstall["WolframChemistry/ProteinVisualization"]
To load the code after installation, evaluate this code:
Needs["WolframChemistry`ProteinVisualization`"]
Paclet Guide
Examples
Basic Examples (8)
BiomoleculePlot3D shows the ribbon diagram of Clostridium perfringens epsilon toxin:
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| Out[1]= |  |
ProteinBackboneAtomPlot shows the backbone atoms of the same structure:
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| Out[2]= |  |
AlphaCarbonPathPlot3D shows the α Carbon trace of proteins:
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| Out[3]= |  |
AmidePlanePlot shows the amide planes in a protein, highlighting the planar geometry of peptide bonds:
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| Out[4]= |  |
DihedralAnglePlot shows the protein backbones (with residue and dihedral angle information) with relevant planes that give rise to dihedral angles ϕ and ψ:
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| Out[5]= |  |
ProteinContactMap gives the map of distances between residues in a protein, nucleic acid or protein nucleic acid complexes:
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| Out[6]= |  |
ProteinContactGraphPlot is an alternative way of representing the contact map of biomolecule structure:
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| Out[7]= |  |
RamachandranPlot gives the map of the dihedral angles of a protein:
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| Out[8]= |  |
Publisher
Disclosures
- Local files
- External services
- Learn More »
Compatibility
Wolfram Language Version 13.0
External Links
- https://www.rcsb.org/
- https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction
- https://en.wikipedia.org/wiki/Dihedral_angle
- https://en.wikipedia.org/wiki/Ramachandran_plot
- https://en.wikipedia.org/wiki/Protein_contact_map
- https://en.wikipedia.org/wiki/Peptide_bond
- http://www.smallscalechemistry.colostate.edu/PowerfulPictures/ProteinStructure.pdf
Version History
- 1.1.2 – 01 March 2024
- 1.1.1 – 20 December 2023
- 1.1.0 – 25 October 2023
- 1.0.1 – 30 May 2023
- 1.0.0 – 26 May 2023