AllMetal3D
Identify likely metal and water binding sites from a protein structure.
Overview
Predict metal and water binding sites in proteins using 3D convolutional neural networks (AllMetal3D/Water3D).
Run AllMetal3D on Neurosnap
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Features
- Predicts metal-binding and water-binding sites directly from an input protein structure using 3D CNNs.
- Provides per-site probabilities for different metal ions and water occupancy.
- Uses a joint model of localization, identity, and coordination geometry to improve metal-site precision.
- Considers local 3D atomic environments rather than only sequence motifs, enabling detection of noncanonical sites.
- Can be applied to experimentally determined and predicted structures (such as AlphaFold models).
- Outputs machine-readable result files for downstream analysis and integration into custom workflows.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access AllMetal3D using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using AllMetal3D in publications or research outputs.
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AllMetal3D, Simon Duerr, Ursula Roethlisberger, BioRxiv, 2024 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |