Metal3D and Metal1D: Accurate prediction of transition metal ion location via deep learning
If using this work please cite:
Accurate prediction of transition metal ion location via deep learning
S.L. Dürr, A. Levy, U. Rothlisberger
bioRxiv 2022.08.22.504853; doi: https://doi.org/10.1101/2022.08.22.504853
For local installation run the following commands to setup the environment.
conda env create -f environment.yml
conda activate metalprediction
cd Metal3D
You need to have VMD installed to view predictions directly from the commandline program (connect with ssh -X if working on a remote machine), download VMD from uiuc.edu.
Alternatively you can use --writecube --cubefile nameofcube.cube --softexit and view the predicted maps in UCSF Chimera or any other viewer that supports cube file.
Typical commands would be:
Analyze all ASP, CYS, ASN, GLN, GLU and HIS residues, write a pdb file with the found probes and write the maximum probabilty to a text file. Will open VMD viewer.
Analyze only specific residues in the pdb file and write a cubefile to disk without openening VMD.
./metal3d.py --pdb PDB.pdb --id 91 94 116 --writecube --cubefile test.cube --softext
Display all possible options
./metal3d.py --help
Data
The PDB codes used for training, validation and testing are available in data.
The PDB codes used for the selectivity analysis including the residue ids of the coordinating residues are available in data as selectivity_analysis_sites.csv.
License
All code is licensed under MIT license, the weights of the network are licensed under CC BY 4.0.
Metal3D and Metal1D: Accurate prediction of transition metal ion location via deep learning
If using this work please cite:
How to run predictions
No installation, no account required use Metal3D on Huggingface Spaces
If you prefer a notebook based environment
Command line usage is described below
How to install and run locally
For local installation run the following commands to setup the environment.
You need to have VMD installed to view predictions directly from the commandline program (connect with ssh -X if working on a remote machine), download VMD from uiuc.edu. Alternatively you can use
--writecube --cubefile nameofcube.cube --softexitand view the predicted maps in UCSF Chimera or any other viewer that supports cube file.Typical commands would be:
Analyze all ASP, CYS, ASN, GLN, GLU and HIS residues, write a pdb file with the found probes and write the maximum probabilty to a text file. Will open VMD viewer.
./metal3d.py --pdb PDB.pdb --metalbinding --writeprobes --probefile metalsites.pdb --maxpAnalyze only specific residues in the pdb file and write a cubefile to disk without openening VMD.
./metal3d.py --pdb PDB.pdb --id 91 94 116 --writecube --cubefile test.cube --softextDisplay all possible options
./metal3d.py --helpData
The PDB codes used for training, validation and testing are available in
data. The PDB codes used for the selectivity analysis including the residue ids of the coordinating residues are available indataasselectivity_analysis_sites.csv.License
All code is licensed under MIT license, the weights of the network are licensed under CC BY 4.0.