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metal-site-prediction
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metal-site-prediction
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# Metal3D and Metal1D: Accurate prediction of transition metal ion location via deep learning [](https://zenodo.org/badge/latestdoi/456988168) [](https://colab.research.google.com/github/lcbc-epfl/metal-site-prediction/blob/main/Metal3D/ColabMetal.ipynb) 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 # How to run predictions No installation, no account required use [Metal3D on Huggingface Spaces](https://hf.space/simonduerr/metal3d) If you prefer a notebook based environment [](https://colab.research.google.com/github/lcbc-epfl/metal-site-prediction/blob/main/Metal3D/ColabMetal.ipynb) Command line usage is described below # How to install and run locally 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](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD). 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. `./metal3d.py --pdb PDB.pdb --metalbinding --writeprobes --probefile metalsites.pdb --maxp ` 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.
