Protein Structure · HeliXon
OmegaFold
Predicts protein structures from single sequences without multiple sequence alignments, suited for orphan proteins.
What OmegaFold is
OmegaFold is a structure prediction tool developed by HeliXon. It predicts three-dimensional protein structures directly from an individual amino acid sequence, eliminating the need to construct multiple sequence alignments (MSAs).
Many comparative and alignment-based modelling methods degrade in accuracy when homologous sequences cannot be found in databases. OmegaFold is designed to address this limitation, providing structural models for orphan sequences, de novo designed proteins, synthetic constructs, and proteins from previously unexplored regions of sequence space.
Key facts
- Version
- 2.0
- Input modality
- Protein sequence
- Output modality
- PDB all-atom coordinates and per-residue pLDDT scores
- GPU memory
- 16 GB
What you can use it for
- Orphan protein structure prediction
- Generating structural models for naturally occurring proteins that have no identifiable sequence homologues in public databases.
- De novo protein design validation
- Predicting the three-dimensional structures of computationally designed proteins lacking evolutionary history.
- Synthetic construct modelling
- Assessing the predicted conformation of engineered or synthetic sequences where alignment-based tools fail.
Run it here
No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.
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OmegaFold
Strengths and limits
Good at
- Predicts all-atom coordinates directly from a single sequence without relying on multiple sequence alignments.
- Functions effectively on de novo designs and orphan proteins where alignment-dependent techniques fail.
- Outputs per-residue pLDDT confidence scores alongside atomic coordinates to indicate structural reliability.
Watch out for
- Requires 16 GB of GPU memory to run.
- Predicted coordinates with per-residue pLDDT values at or below 70 are generally not reliable.
Inputs and outputs
You provide
Protein sequence
Single-letter amino acid code. Whitespace and FASTA headers are stripped automatically.
You get back
All-atom coordinates in PDB format, viewable and downloadable.
pLDDT score per residue (0–100). Above 70 is generally reliable.
Licence
Commercial use permitted · Apache-2.0
The Apache-2.0 licence allows use in commercial research and products.
Questions
Can I use OmegaFold commercially?
Commercial use permitted. The Apache-2.0 licence allows use in commercial research and products.
How do I run OmegaFold without installing anything?
Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers on 1× A100 16GB, typically in 12s, and a run costs about 70 credits. Visitors without an account get 1,000 credits a month.
Does OmegaFold require sequence homologues or alignments?
No. OmegaFold is an MSA-free method that predicts structural coordinates using only a single input sequence.
What output files and confidence metrics are generated?
It outputs all-atom coordinates in standard PDB format along with a per-residue pLDDT vector scaled from 0 to 100.
How should the output confidence score be interpreted?
Residues with a pLDDT score above 70 are generally considered reliable.
What hardware is necessary to run OmegaFold?
OmegaFold requires a GPU with at least 16 GB of memory.
Written from OmegaFold's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.