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Structure prediction of alternative protein conformations

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Cfold

Colab (run in the web)

Colab Notebook

Local installation

Python packages

  • For the python environment, we recommend to install it with pip as described below.
    You can do this in your virtual environment of choice.
pip install -U jaxlib==0.3.24+cuda11.cudnn82 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
pip install jax==0.3.24
pip install ml-collections==0.1.1
pip install dm-haiku==0.0.9
pip install pandas==1.3.5
pip install biopython==1.81
pip install chex==0.1.5
pip install dm-tree==0.1.8
pip install immutabledict==2.0.0
pip install numpy==1.21.6
pip install scipy==1.7.3
pip install tensorflow-cpu==2.12.0
pip install tensorflow==2.11.0
pip install optax==0.1.4

Get network parameters for Cfold

wget https://gitlab.com/patrickbryant1/cfold_data/-/raw/main/params10000.npy

Uniclust30

wget http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz --no-check-certificate
mkdir data/uniclust30
mv uniclust30_2018_08_hhsuite.tar.gz data/uniclust30
tar -zxvf data/uniclust30/uniclust30_2018_08_hhsuite.tar.gz

HHblits

git clone https://github.com/soedinglab/hh-suite.git
mkdir -p hh-suite/build && cd hh-suite/build
cmake -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
cd ..

Run the test case

Search Uniclust30 with HHblits to generate an MSA

ID=4AVA
FASTA_DIR=./data/test/
UNICLUST=./data/uniclust30_2018_08/uniclust30_2018_08
OUTDIR=./data/test/

./hh-suite/build/bin/hhblits -i $FASTA_DIR/$ID.fasta -d $UNICLUST -E 0.001 -all -oa3m $OUTDIR/$ID'.a3m'

MSA feats

MSA_DIR=./data/test/
OUTDIR=./data/test/

python3 ./src/make_msa_seq_feats.py --input_fasta_path $FASTA_DIR/$ID'.fasta' \
--input_msas $MSA_DIR/$ID'.a3m' --outdir $OUTDIR

Predict

FEATURE_DIR=./data/test/
PARAMS=./params10000.npy
OUTDIR=./data/test/

NUM_REC=3 #Increase for hard targets
NUM_SAMPLES=13 #Increase for hard targets

python3 ./src/net/predict_with_clusters.py --feature_dir $FEATURE_DIR \
--predict_id $ID \
--ckpt_params $PARAMS \
--num_recycles $NUM_REC \
--num_samples_per_cluster $NUM_SAMPLES \
--outdir $OUTDIR/

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Structure prediction of alternative protein conformations

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