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.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
Retrieving Your Protein Sequence
The AlphaFold engine requires a single cohesive amino acid sequence as input. The recommended source is UniProt.Search UniProt
Navigate to UniProt and search for the gene of interest. Select the human isoform where relevant.
Check for an Existing AlphaFold Structure
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.
Running an AlphaFold Pipeline
Name Your Pipeline
Enter a descriptive pipeline name (e.g.,
EGFR-alphafold-canonical). This name will identify the run in your pipeline history.Enter Your Sequence
Paste your amino acid sequence into the sequence input field. Ensure it is in a single cohesive line with no breaks or spaces.
Configure Advanced Parameters
Advanced parameters are pre-set to optimized defaults. Unless you have a specific reason to modify them, leave these as-is and proceed.
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.Next Steps
With your AlphaFold structure in hand, the typical workflow continues:- RevPocket — Identify druggable binding sites on your predicted structure before running docking
- RevScreen - Static & Flexible Docking — Run virtual screening campaigns against your defined binding pocket
- RevScreen - Ensemble Docking — Use MD-sampled protein conformations for maximum-accuracy screening
- RevMD-Bind — Validate binding stability of top candidates with protein-ligand MD simulation