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README.md

Programmed trade-offs in protein folding networks

Sebastian Pechmann (2020)

Department of Biochemistry, University of Montreal

pechmannlab.net

1. Structural classification of chaperone substrates

structural_classification.py

2. Homology modeling

homology_modelling.py

3. Minimization of PDB structures

preparePDB.py

4. Compute structural phylogeny with 'superpose'

structphylo.py

5. Compute structure-based multiple-sequence alignment with 'Stamp'

structaln.py

6. Contact maps of hydrophobic contacts with 'CSU'

csu.py

7. Analysis of protein contact networks

protein_network.py

8. Analysis of binding motifs and discriminative peptide sequences

binding_meme.py binding_motifs.py

9. Analysis of codon usage

rarecodons.py

10. Integrated analysis

tradeoff_tree.py

Dependencies:

R: ggplot2, reshape2, pROC, viridis, cowplot, , MASS, rpart, ape, ggExtra, matrixStats, ggpubr

Python: numpy, pandas, networkx, subprocess, Biopython, itertools, sklearn, multiprocessing, random, glob, MODELLER, re, shutil, Weblogo

External: superpose, STAMP, DSSP, CSU, MEME, Weblogo

(to be updated)

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