3D Protein Structure Prediction Server AlphaFold 3
The AlphaFold Server is a free, web-based platform launched by Google DeepMind and Isomorphic Labs to provide the scientific community with access to AlphaFold 3.
While the original AlphaFold was revolutionary for predicting protein structures, the AlphaFold 3 server expands this capability to virtually all “life’s molecules,” allowing researchers to model how proteins interact with DNA, RNA, ligands, and more in a single, unified system.
🧬 Key Capabilities
Unlike its predecessors, the AlphaFold 3 server is a multimodal model. It doesn't just fold proteins; it predicts the joint 3D structure of complex molecular assemblies.
- Protein-Ligand Interactions: Accurately models how small molecules (drugs) bind to proteins, showing a 50% improvement over traditional docking methods.
- Nucleic Acids: Predicts the structures of DNA and RNA and how they interact with proteins (e.g., transcription factors or CRISPR complexes).
- Chemical Modifications: Predicts the structures of DNA and RNA and how they interact with proteins (e.g., transcription factors or CRISPR complexes).
- Ions and Hydration: Models the binding of essential ions (like Mg2+ or Zn2+) that stabilize biological structures.
🛠️ How the Server Works
The server is designed to be accessible to biologists without requiring extensive coding or high-end local hardware.
- Input: Users enter amino acid sequences (for proteins) or nucleotide sequences (for DNA/RNA).
- Ligands: Small molecules can be selected from a predefined list or specified using SMILES strings.
- Generative Diffusion: Behind the scenes, AlphaFold 3 uses a Diffusion Module (similar to AI image generators). It starts with a “cloud” of random atoms and iteratively refines them into a highly accurate 3D structure.
- Output: The server provides a downloadable
.ciffile and interactive 3D visualizations, along with confidence scores.
📊 Understanding Confidence Scores
The server provides four primary metrics to help you judge if a prediction is reliable:
| Metric | Full Name | What it Measures |
|---|---|---|
| pLDDT | Predicted Local Distance Difference Test | Confidence in the local position of individual atoms (Scale: 0–100). |
| PAE | Predicted Aligned Error | Confidence in the relative orientation between two different parts of the complex. |
| pTM | Predicted TM-score | Overall confidence in the global fold of the entire structure. |
| ipTM | Interface pTM | Specific confidence in the accuracy of the interaction interface between molecules. |
⚠️ Usage & Restrictions
Unlike its predecessors, the AlphaFold 3 server is a multimodal model. It doesn't just fold proteins; it predicts the joint 3D structure of complex molecular assemblies.
- Non-Commercial Only: The server is strictly for academic and non-commercial research. Commercial entities must license the technology through Isomorphic Labs.
- Daily Limits: To ensure fair access, there is a daily limit on the number of jobs a user can submit.
- Chemical Modifications: Predicts the structures of DNA and RNA and how they interact with proteins (e.g., transcription factors or CRISPR complexes).
- No Water/Hydrogens: It does not currently predict the positions of water molecules or hydrogen atoms.
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