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This is a Bayesian model for sequence and structure alignment of multiple proteins in a star phylogeny. The structural divergence across time is modelled by letting the dihedral angles of the backbones evolve according to a diffusion over the flat square torus.

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nifetsnifets
Update README.md
Jun 20, 2023
af72900 · Jun 20, 2023

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.VSCodeCounter/2023-04-28_12-00-52
Apr 28, 2023
.ipynb_checkpoints
.ipynb_checkpoints
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.vscode
.vscode
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archive
archive
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data
data
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images
images
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listings
listings
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src
src
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test
test
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.gitattributes
.gitattributes
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.gitignore
.gitignore
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Ancestor Reconstruction.ipynb
Ancestor Reconstruction.ipynb
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Bisection.ipynb
Bisection.ipynb
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Globins Experiment.ipynb
Globins Experiment.ipynb
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Manifest.toml
Manifest.toml
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Pair Parameter Inference.ipynb
Pair Parameter Inference.ipynb
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Project.toml
Project.toml
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ProteinViewer.ipynb
ProteinViewer.ipynb
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README.md
README.md
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Simulated Data Experiments.ipynb
Simulated Data Experiments.ipynb
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Simulated Experiment.ipynb
Simulated Experiment.ipynb
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Triple Parameter Inference.ipynb
Triple Parameter Inference.ipynb
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Untitled.ipynb
Untitled.ipynb
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chain-file.jls
chain-file.jls
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evol_traj_globins.png
evol_traj_globins.png
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jumpingdiff.png
jumpingdiff.png
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persistence.png
persistence.png
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simulated data.png
simulated data.png
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test.ipynb
test.ipynb
May 18, 2023

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(WIP) Sequence and structure evolution model for proteins

  • statistical alignment
  • torsional angle diffusion

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This is a Bayesian model for sequence and structure alignment of multiple proteins in a star phylogeny. The structural divergence across time is modelled by letting the dihedral angles of the backbones evolve according to a diffusion over the flat square torus.

Topics

protein-structure bayesian-inference gibbs-sampling sequence-alignment structure-alignment monte-carlo-sampling

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