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Related Experiment Video

Updated: May 1, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

This summary is machine-generated.

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.

Keywords:

Evolution FoldSeek Protein structure Structural phylogeny Twilight zone

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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.