Related Experiment Video
Updated: May 1, 2026
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
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A Pipeline for Generating Datasets of Three-Dimensional Tertiary Interaction Characters for Model-Based Structural
Nicholas J Matzke1, Caroline Puente Lelievre2, Matthew A B Baker3
1School of Biological Sciences, The University of Auckland, Auckland, New Zealand. n.matzke@auckland.ac.nz.
Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2026
Summary
Tertiary-interaction (3Di) characters, derived from protein structure predictions, can now be used for phylogenetic inference alongside amino acid sequences. An R script pipeline automates the creation of joint alignment files for this novel phylogenetic analysis method.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Phylogenetics
Background:
- Tertiary-interaction (3Di) characters were developed for protein structure homology searches using FoldSeek.
- These 3Di characters represent structural information and have potential applications beyond homology searching.
Purpose of the Study:
- To adapt 3Di characters for model-based phylogenetic inference using Maximum Likelihood methods.
- To develop a practical computational pipeline for integrating 3Di and amino acid (AA) characters in phylogenetic analyses.
Main Methods:
- Protein structure prediction files were converted into 3Di characters.
- Amino acid sequences were combined with 3Di characters.
- R scripts were utilized to automate the alignment and joining of AA and 3Di data into a partitioned file.
Main Results:
- A functional pipeline was created to automate the generation of joint AA+3Di alignment files.
- Example scripts and explanations of R functions for this process are provided.
Conclusions:
- The developed pipeline facilitates the practical use of 3Di characters in phylogenetic analyses for medium to large datasets.
- This approach enables a novel method for phylogenetic inference by combining structural and sequence data.
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