Wolfram Function Repository
Instant-use add-on functions for the Wolfram Language
Function Repository Resource:
Visualize the intrinsically disordered regions (IDRs) in a protein
ResourceFunction["BioMoleculeIDRPlot3D"][protein] shows the 3D structure of protein with the intrinsically disordered regions highlighted. | |
ResourceFunction["BioMoleculeIDRPlot3D"][protein,"AveragePredictionConfidence"] shows protein with coloring based on the averaged confidence of disorder prediction. |
ColorRules | <|"Disordered"→Lighter@Red,"Folded"→Lighter@Blue|> | rules to color different regions of a protein |
ColorFunction | "RedBlueTones" | color scheme when residues are colored by the averaged confidence of prediction |
Visualize the disordered and folded regions of MDC1 (Mediator of DNA damage checkpoint protein 1):
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Visualize the average confidence of prediction for the same protein:
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Visualize the disordered and folded region of a BioSequence:
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Also show its averaged prediction confidence:
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Visualize the disordered and folded regions of a protein from the ESM Metagenomic Atlas:
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Visualize the structure of the disordered and folded regions of a BioMolecule:
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Set colors for different regions:
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"ConfidenceCutoff" determines how long the disordered regions will be:
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Minimum length for IDRs can be set by using "MinIDRLength":
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Here are some common UniProt IDs of human proteins with significant disorder:
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Visualizing the disordered (red) regions for these proteins (columns 1, 3 and 5) and how it is connected to average confidence of prediction (red for lower values and blue for higher values in columns 2, 4 and 6). This code takes a while to evaluate:
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For invalid BioSequence inputs for which structures cannot be predicted Failure with an error message is returned:
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Visualize the disordered regions in a protein in human code by FAM184A gene:
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Visualize the average confidence of prediction in the protein:
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