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BioMoleculeAlign[ref,biomol]

returns a copy of biomol that has been aligned with reference biomolecule ref.

BioMoleculeAlign[ref,biomol,mapping]

uses the supplied mapping to determine which chains to include in the alignment.

BioMoleculeAlign[ref,biomol,mapping,prop]

aligns the biomolecules and returns the property prop of the alignment.

Details
Details and Options Details and Options
Examples  
Basic Examples  
Scope  
Neat Examples  
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BioMoleculeAlign

BioMoleculeAlign[ref,biomol]

returns a copy of biomol that has been aligned with reference biomolecule ref.

BioMoleculeAlign[ref,biomol,mapping]

uses the supplied mapping to determine which chains to include in the alignment.

BioMoleculeAlign[ref,biomol,mapping,prop]

aligns the biomolecules and returns the property prop of the alignment.

Details

  • BioMoleculeAlign is used to structurally align two peptide or nucleic acid molecules in space.
  • BioMoleculeAlign uses a structure-based sequence-independent algorithm to align 3D structures by optimizing the template-modeling score objective function, or TM-score. It is often used when comparing a predicted structure to an experimentally determined structure.
  • The TM-score for a given alignment is defined by ∑i, where Lref is the length of the reference structure, di is the distance between backbone atoms for the ith aligned residue, and d0(Lref)=1.24-1.8 is a distance scale to normalize the result. The alignment that maximizes the TM-score is returned.
  • The TM-score lies between 0 and 1, where 1 indicates a perfect match. A TM-score below 0.2 is considered to be from random chance, while a score over 0.5 indicates a roughly the same folding.
  • mapping should be either Automatic or a rule between chain labels in ref and biomol, e.g. {"A","B"}{"C","D"}. When a rule is given, only the specified chains will be considered in the alignment.
  • prop can be one of the following:
  • "BioMolecule"the aligned biomolecule
    "Transformation"the transformation function used
    "RMSError"the alignment root mean squared error
    "TMScore"the template-modeling score for the alignment
    "AlignedResidueCount"the number of residues aligned
    "SequenceIdentity"fraction of aligned residues that are identitical
    "SequenceCharacterAlignment"a visual representation of the aligned sequences
    Allan Association with all properties

Examples

open all close all

Basic Examples  (3)

Create a biomolecule based on an experimental crystal structure:

Wolfram Language code: experimental = Import["ExampleData/1PPT.pdb"]

Now take the peptide sequence from that biomolecule and fold it:

Wolfram Language code: predicted = BioMolecule[First[experimental["BioSequences"]]]

The predicted structure's 3D coordinates are unrelated to the experimental structure:

Wolfram Language code: BioMoleculePlot3D[{experimental, predicted}]

Now align the predicted structure with the experimental structure and show them in 3D:

Wolfram Language code: BioMoleculePlot3D[{experimental, BioMoleculeAlign[experimental, predicted]}]

Align a smaller peptide to a specific chain in a larger peptide:

Wolfram Language code: bm1 = BioMolecule[«1»]; bm2 = BioMolecule[«1»]; BioMoleculePlot3D[{bm1, BioMoleculeAlign[bm1, bm2, "B3" -> "A"]}]

Align the smaller peptide to a different chain:

Wolfram Language code: BioMoleculePlot3D[{bm1, BioMoleculeAlign[bm1, bm2, "A2" -> "A"]}]

BioMoleculeAlign can align peptides with dissimilar sequences but similar 3D structures:

Wolfram Language code: bm1 = BioMolecule[ExternalIdentifier["PDBStructureID", "101M"]]; bm2 = BioMolecule[ExternalIdentifier["PDBStructureID", "1AZI"]]; alignmentData = BioMoleculeAlign[bm1, bm2, Automatic, All]; BioMoleculePlot3D[{bm1, alignmentData["BioMolecule"]}]

The structures are aligned very well as shown by the low RMSD error and high TM-score:

Wolfram Language code: alignmentData[[{"RMSError", "TMScore"}]]

Nearly all the amino acid residues participate in the alignment:

Wolfram Language code: alignmentData["SequenceCharacterAlignment"]

But there are significant differences in the two sequences:

Wolfram Language code: SequenceAlignment[First[bm1["BioSequences"]], First[bm2["BioSequences"]]]

Scope  (2)

Align an RNA strand to the RNA portion of an RNA-peptide complex:

Wolfram Language code: ref = BioMolecule[«1»]; rna = BioMolecule[«1»]; aligned = BioMoleculeAlign[ref, rna]
Wolfram Language code: BioMoleculePlot3D[{ref, aligned}]

Compare the structures of Cyclin-dependent kinase 2 from two different organisms from AlphaFold Database:

Wolfram Language code: bm1 = ServiceExecute["AlphaFoldDatabase", "BioMolecule", {"UniProtID" -> "A0A2K6V5L6"}]; bm2 = ServiceExecute["AlphaFoldDatabase", "BioMolecule", {"UniProtID" -> "A0A2K6GY84"}]; bma = BioMoleculeAlign[bm1, bm2]; BioMoleculePlot3D[{bm1, bma}, PlotLegends -> {"BioMolecule 1", "Aligned BioMolecule 2"}]

Neat Examples  (1)

Align two large biomolecular assemblies:

Wolfram Language code: bm1 = BioMolecule[ExternalIdentifier["PDBStructureID", "1PV8"]]["Assemblies"][[1]]; bm2 = BioMolecule[ExternalIdentifier["PDBStructureID", "1E51"]]["Assemblies"][[1]]; bma = BioMoleculeAlign[bm1, bm2]
Wolfram Language code: colors = {RGBColor[0.6666666666666666, 0.6666666666666666, 0.6666666666666666], RGBColor[7/9, 1/3, 1/3]}; BioMoleculePlot3D[{Style[bm1, RGBColor[0.6666666666666666, 0.6666666666666666, 0.6666666666666666]], Style[bma, RGBColor[7/9, 1/3, 1/3]]}, PlotLegends -> {"BioMolecule 1", "Aligned BioMolecule 2"}]
Wolfram Research (2025), BioMoleculeAlign, Wolfram Language function, https://reference.wolfram.com/language/ref/BioMoleculeAlign.html.

Text

Wolfram Research (2025), BioMoleculeAlign, Wolfram Language function, https://reference.wolfram.com/language/ref/BioMoleculeAlign.html.

CMS

Wolfram Language. 2025. "BioMoleculeAlign." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/BioMoleculeAlign.html.

APA

Wolfram Language. (2025). BioMoleculeAlign. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioMoleculeAlign.html

BibTeX

@misc{reference.wolfram_2026_biomoleculealign, author="Wolfram Research", title="{BioMoleculeAlign}", year="2025", howpublished="\url{https://reference.wolfram.com/language/ref/BioMoleculeAlign.html}", note=[Accessed: 12-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_biomoleculealign, organization={Wolfram Research}, title={BioMoleculeAlign}, year={2025}, url={https://reference.wolfram.com/language/ref/BioMoleculeAlign.html}, note=[Accessed: 12-June-2026]}