> ## Documentation Index
> Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt
> Use this file to discover all available pages before exploring further.
# AlphaFold
> Predict the 3D structure of a protein from its amino acid sequence using Revilico's AlphaFold engine
## Overview
**AlphaFold** is Revilico's protein structure prediction engine. It takes a raw amino acid sequence as input and generates the full 3D structure of the protein — enabling downstream analyses like pocket identification, docking, and MD simulation without requiring an experimental crystal structure.
This is the starting point for any target-based drug discovery campaign where no experimental structure is available.
[Exploring the AlphaFold Workflow for Protein Structure Prediction — Watch Video](https://www.loom.com/share/35a1d1492f3d4a7e8e664546f09febc9)
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## How AlphaFold Works
AlphaFold predicts a protein's 3D structure directly from sequence. The core breakthrough is that it solves the protein folding problem — mapping a linear amino acid sequence to the precise three-dimensional geometry that determines the protein's function and druggability.
Every engine in Revilico includes documentation on the right-hand side of the interface:
* **Documentation** — an overview of what the engine does and its scientific context
* **Configuration** — a step-by-step guide through the input parameters
* **Revilico Guide** — AI-powered assistant that searches through Revilico documentation and suggests answers to your questions
* **Interpreter** — reads your screen and helps interpret outputs across different engines
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## Retrieving Your Protein Sequence
The AlphaFold engine requires a **single cohesive amino acid sequence** as input. The recommended source is **UniProt**.
Navigate to [UniProt](https://www.uniprot.org/) and search for the gene of interest. Select the human isoform where relevant.
On the UniProt entry page, scroll to the **Structure** section. If an AlphaFold structure already exists for your protein, you can download it directly — skipping the need to run a new prediction. Review the available variants (canonical, isoforms, etc.) and choose the one appropriate for your target.
If no pre-computed structure is available, go to the **Sequence** tab and copy the full amino acid sequence.
The engine requires the sequence in a **single unbroken line** with no spaces, line breaks, or irregular characters. If your sequence is formatted with breaks or whitespace, use the Revilico Interpreter to reformat it into a clean single-line string before pasting it in.
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## Running an AlphaFold Pipeline
From the Revilico OS dashboard, open the AlphaFold engine.
Enter a descriptive pipeline name (e.g., `EGFR-alphafold-canonical`). This name will identify the run in your pipeline history.
Paste your amino acid sequence into the sequence input field. Ensure it is in a single cohesive line with no breaks or spaces.
If your sequence contains irregularities, paste it into the Revilico Interpreter and ask it to reformat the sequence into a single clean line.
Advanced parameters are pre-set to optimized defaults. Unless you have a specific reason to modify them, leave these as-is and proceed.
Click **Run Pipeline**. You will see a confirmation that the pipeline has been created and queued.
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## Monitoring and Viewing Results
Once your pipeline is created, track it from the **Command Center** — the central hub for all pipeline activity.
### Checking Pipeline Status
Navigate to the Command Center from the top navigation. Your AlphaFold run will appear with its current status. You can monitor multiple pipelines simultaneously from this view.
### Viewing 3D Structure Output
When the run completes, open the results from the Command Center:
| Output | Description |
| ----------------------- | ----------------------------------------------------------------------------------- |
| **3D Structure Viewer** | Interactive visualization of the predicted protein structure |
| **Rank Number** | Model confidence ranking — lower rank numbers indicate higher-confidence structures |
| **3D Settings** | Adjust rendering, visibility, and coloring of the structural model |
| **Analytics** | Confidence metrics (pLDDT scores) and structural quality measures |
### Downloading the Structure
Click **Download** to export the predicted structure as a PDB file. This file can be used directly as input for downstream Revilico engines including RevPocket, RevScreen, and RevMD.
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## Next Steps
With your AlphaFold structure in hand, the typical workflow continues:
* [**RevPocket**](/tutorials/rev-target/revpocket) — Identify druggable binding sites on your predicted structure before running docking
* [**RevScreen - Static & Flexible Docking**](/tutorials/rev-bind/static-flexible-docking) — Run virtual screening campaigns against your defined binding pocket
* [**RevScreen - Ensemble Docking**](/tutorials/rev-bind/ensemble-docking) — Use MD-sampled protein conformations for maximum-accuracy screening
* [**RevMD-Bind**](/docs/revmd-bind) — Validate binding stability of top candidates with protein-ligand MD simulation