/TMH_insertion_energy

Inferring TMH insertion energies

Primary LanguageHTMLGNU General Public License v3.0GPL-3.0

TMH_insertion_energy

Inferring TMH insertion energies from reference sequences with known helix positions

Data

Folder/ File Description
reference_sequences Reference sequences and corresponding HHM-profiles
sequences Sequences in fasta format
profiles HHM-profiles created with hhblits against the UniRef30 database
hhalign_X HMM-HMM alignment of every profile against reference profile X
dgpred_results Inferred helices and corresponding dgpred energy calculations
sequences.fasta All sequences in one fasta file
TMH_insertion_energies.xlsx Energy values and sequences for 19 residue window and full length helices

Scripts

The python3 script fasta_to_helices.py takes as input a list of sequences in fasta format, corresponding HMM-profiles and HMM-HMM-alignments and infers the helices based on reference sequences with annotated structural information and calculates the corresponding energy values using dgpred.