Predicting a batch of protein structures
We recently installed RoseTTAFold on our server. What a powerful tool! I want to share with you a routine to predict a protein structure for every protein sequence in a batch.
# follow the directions to install RoseTTAFold:
# https://github.com/RosettaCommons/RoseTTAFold
# in the RoseTTAFold installation directory,
# create a subdirectory for protein structure predictions and enter that subdirectory
mkdir predictions && cd predictions
# move all your protein sequence fasta files into this subdirectory
# activate the RoseTTAFold conda environment
conda activate RoseTTAFold
# for each protein sequence in this directory,
# use RoseTTAFold to predict a protein structrue
for i in $(ls *.fasta | sed 's/.fasta//')
do
mkdir ${i}_output
../run_e2e_ver.sh ${i}.fasta ${i}_output
mv ${i}_output/t000_.e2e.pdb ${i}.pdb
done