Configure:
FASTA Sequence Paste or load a sequence, with or without header. One may insert path to a file or load from disk.
Submit and Analysis (Buttons)
#!/bin/bash # QwikFold install instructions for AlphaFold # # Diego E. B. Gomes | dgomes@auburn.edu # Rafael C. Bernardi | rcbernardi@auburn.edu # # Install alphafold 2 - Ubuntu 18.04. # https://github.com/deepmind/alphafold # Step 0 - Modify these paths according export ALPHAFOLD_DATASETS='/data/alphafold_dbs/' # Step 1 - create a conda environment conda create -n af2 python=3.8 -y # Step 2 - activate the environment conda activate af2 # Step 3 - Clone Alphafold from GitHub into THIS folder. git clone https://github.com/deepmind/alphafold.git # Step 4 - Download chemical properties to the common folder wget -q -P alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt # Step 5 - Go to AlphaFold folder, and set path to current DIR cd alphafold alphafold_path=${PWD} # Step 6 - Install required packages conda install -y -c nvidia cudnn==8.0.4 conda install -y -c bioconda hmmer hhsuite==3.3.0 kalign2 conda install -y -c conda-forge openmm=7.5.1 pdbfixer pip # Step 7 - Upgrade PIP pip3 install --upgrade pip # Step 8 - Install additional AlphaFold requirements using PIP pip3 install -r ./requirements.txt pip3 install --upgrade "jax[cuda111]" -f https://storage.googleapis.com/jax-releases/jax_releases.html # Step 9 - Apply patch to OpenMM python_path=$(which python) cd $(dirname $(dirname ${python_path}))/lib/python3.8/site-packages patch -p0 < ${alphafold_path}/docker/openmm.patch # Step 10 (very slow) - Download AlphaFold datasets (reduced datasets ~/400Gb) if [ ! -d ${ALPHAFOLD_DATASETS} ] ; then mkdir -p ${ALPHAFOLD_DATASETS} fi # Step 11 - Download Alphafold reduced datasets ( ~400Gb) cd ${alphafold_path} bash scripts/download_all_data.sh ${ALPHAFOLD_DATASETS} reduced_dbs # Step 12 - Download Alphafold complete datasets ( ~2.2Tb ) cd ${alphafold_path} bash scripts/download_all_data.sh ${ALPHAFOLD_DATASETS}