A ME-model framework to simulate the response of E. coli under acid stress

• python == 2.7
• pandas >= 0.21.0
• numpy >= 1.13.3
• cobrame >= 0.0.8
• cobrapy == 0.5.11
• biopython >= 1.60

For more information on solving the ME-model, please refer to cobrame package. The related paper has been published at PLOS Computational Biology.

• /proteins, a directory that contains the information about the periplasmic proteins of E. coli as described by the ME-model, including protein structure (prot.pdb) and the calculated charges of the folded protein and its side chains under different pH values (sum_crg.out).
• b3509.fasta, sequence of the hdeB gene.
• charged_aa_side_chain_pKa.csv, table of individual amino acid side chain pKa values, used to calculate the charge of unfolded protein (peptide) at different pH values.
• lipid_fatty_acid_composition_under_acid.csv, relative fraction of membrane lipids with different fatty acid tails in terms of non-adapted and acid-adapted profiles.
• peptide_radius_of_gyration.csv, table of empirical measurements on the radius of gyration of peptides.
• periplasm_protein_fold_rate.csv, fold rates of periplasmic proteins, more information on how protein fold rate is calculated can be found in ssbio package.