Require python>=3.7
Clone the repository and install it
git clone https://github.com/zw2x/glinter.git
cd glinter
pip install -e .Manually install the following softwares and models
The taxonomy database can be found at
The following commands are executed in the repository glinter.
Replace the environment variables in set_env.sh and run.sh in the scripts directory
by your installation paths and then run
source scripts/set_env.shThere are two example pdb files in the examples directory.
To predict the inter-protein heterodimeric contacts between 1a59A.pdb and 1a59B.pdb, run
scripts/build_hetero.sh examples/1a59A.pdb examples/1a59B.pdb examples/To predict the inter-protein homodimeric contacts between 1a59A.pdb and 1a59B.pdb,
and use 1a59B as the representative monomer (only build MSA for 1a59B), run
scripts/build_homo.sh examples/1a59A.pdb examples/1a59B.pdb examples/ 1a59BMake sure the names of the receptor and ligand are different.
For heterodimers, the raw outputs are examples/1a59A:1a59B/1a59A:1a59B.out.pkl and
examples/1a59A:1a59B/1a59B:1a59A.out.pkl (both directions).
For homodimers, the raw output is examples/1a59A:1a59B/1a59A:1a59B.out.pkl.
For both cases, the final score (the probability that a pair of residue positions is in contact)
is examples/1a59A:1a59B/score_mat.pkl.
The ranked list of residue position pairs is examples/1a59A:1a59B/ranked_pairs.txt;
the first column is the positions in the receptor,
the second column is the positions in the ligand,
the third column is the probability.
See alphafold/example_run.sh for using GLINTER given the predicted structures
from AlphaFold.
Please use the uniclust database
A3M_SpecBloc requires the header of each hit starts with tr| and contains OS=$TAX,
$TAX is the taxonomy name.
Please use the model provided in the repo ckpts/glinter1.pt instead of the one from zenodo