# See how your RNA folds and binds

Predict secondary and 3D structures, compare RNA–RNA interactions, and screen small molecules against RNA targets.

[Get a demo](https://proteiniq.io/contact/sales)[Start free](https://proteiniq.io/app/workflows/templates?template=rna-structure-prediction-method-panel)

1. ## Secondary structure and accessibility

   Predict minimum-energy and alternative folds, pairing probabilities and local accessibility from sequence.

   - [![RNAfold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAfold Predict RNA secondary structures with ViennaRNA. Get MFE structures and plots, or enable the partition function for ensemble results. Sign in to run your sequences.](https://proteiniq.io/app/rnafold)
   - [![RNAsubopt](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAsubopt Enumerate suboptimal RNA secondary structures.](https://proteiniq.io/app/rnasubopt)
   - [![RNAplfold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAplfold Calculate local RNA base-pair probabilities.](https://proteiniq.io/app/rnaplfold)
   - [![ViennaRNA](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### ViennaRNA Predict and analyze RNA secondary structures.](https://proteiniq.io/app/viennarna)
   - [![RNAalifold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAalifold Predict consensus RNA secondary structures from sequence alignments.](https://proteiniq.io/app/rnaalifold)
   - [![RNALfold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNALfold Find locally stable RNA structures in long sequences.](https://proteiniq.io/app/rnalfold)
   - [![RNAdos](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAdos Calculate RNA density-of-states energy distributions.](https://proteiniq.io/app/rnados)
2. ## RNA interaction analysis

   Predict joint folds, duplexes and accessible binding sites for two RNA sequences.

   - [![RNAcofold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAcofold Predict RNA-RNA dimer secondary structures.](https://proteiniq.io/app/rnacofold)
   - [![RNAduplex](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAduplex Predict RNA duplex hybridization between two sequences.](https://proteiniq.io/app/rnaduplex)
   - [![RNAup](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAup Predict RNA-RNA interactions using accessibility-aware energy scoring.](https://proteiniq.io/app/rnaup)
   - [![RNAplex](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAplex Predict query-target RNA interactions quickly.](https://proteiniq.io/app/rnaplex)
3. ## Three-dimensional modeling

   Build 3D models with several structure predictors and compare their confidence.

   - [![Chai-1](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fchai-1.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### Chai-1 Predict 3D structures for proteins, ligands, DNA, RNA, and multi-component complexes.](https://proteiniq.io/app/chai-1)
   - [![Boltz-2](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fboltz-2.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### Boltz-2 Predict biomolecular complex structures and binding affinities for proteins, ligands, DNA, and RNA.](https://proteiniq.io/app/boltz-2)
   - [![OpenFold3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fopenfold-3.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### OpenFold3 Open-source AlphaFold3-based structure prediction for proteins, ligands, DNA, and RNA](https://proteiniq.io/app/openfold-3)
   - [![Protenix](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fprotenix.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### Protenix Open-source biomolecular structure prediction with Protenix](https://proteiniq.io/app/protenix)
   - [![OpenDDE](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fopendde.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### OpenDDE All-atom biomolecular structure prediction](https://proteiniq.io/app/opendde)
   - [![RosettaFold3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Frosettafold3.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RosettaFold3 Open-source structure prediction for proteins, nucleic acids, and ligands](https://proteiniq.io/app/rosettafold3)
   - [![Boltz-2.1](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fboltz-2-1.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### Boltz-2.1 Structure and binding prediction for proteins, DNA, RNA and ligands.](https://proteiniq.io/app/boltz-2-1)
4. ## Design and compound screening

   Design sequences for a target fold, or score how small molecules bind your RNA.

   - [![RNAinverse](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAinverse Design RNA sequences that fold into target structures.](https://proteiniq.io/app/rnainverse)
   - [![RNAdistance](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAdistance Compare RNA secondary structures by base-pair and tree distance.](https://proteiniq.io/app/rnadistance)
   - [![SMRTnet](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fsmrtnet.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### SMRTnet Predict small molecule-RNA interactions using RNA secondary structure with deep learning](https://proteiniq.io/app/smrtnet)
   - [![RNAeval](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAeval Evaluate RNA secondary-structure free energy.](https://proteiniq.io/app/rnaeval)
   - [![RNAplot](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fviennarna.webp&w=96&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) ### RNAplot Visualize RNA secondary structures from dot-bracket inputs.](https://proteiniq.io/app/rnaplot)

## RNA discovery use cases

Pick the method that fits your question and evidence. Each one comes with a workflow you can open and edit.

- [RNA structure prediction Choose the RNA prediction workflow that matches the biological question: intramolecular base pairing, atomic 3D coordinates, or intermolecular RNA binding. See workflow](https://proteiniq.io/use-cases/rna-structure-prediction)
- [RNA secondary structure prediction Predict RNA base pairing, minimum-free-energy structures, alternative folds, and local accessibility from sequence. See workflow](https://proteiniq.io/use-cases/rna-secondary-structure-prediction)
- [RNA 3D structure prediction Generate and compare atomic RNA structure hypotheses with multiple biomolecular foundation models. See workflow](https://proteiniq.io/use-cases/rna-3d-structure-prediction)
- [RNA–RNA interaction prediction Compare joint folding, duplex hybridization, accessibility-aware binding, and fast query–target screening for two RNAs. See workflow](https://proteiniq.io/use-cases/rna-rna-interaction-prediction)

[See all use cases](https://proteiniq.io/use-cases)

## Guides for RNA work

Background guides on the methods, scores, and numbers behind these workflows.

- [![Illustrations of messenger RNA, ribosomal RNA and transfer RNA.](https://proteiniq.io/_next/image?url=%2Fimages%2Fguides%2Fhow-many-types-of-rna-are-there%2Ffeatured.webp&w=1920&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) Genetics · 5 min ### How many types of RNA are there? There are three major RNA types: mRNA, rRNA, and tRNA. rRNA is the most abundant by mass, tRNA is the smallest of the three, and mRNA can be the longest.](https://proteiniq.io/guides/how-many-types-of-rna-are-there)
- [![Single RNA strand breaking into smaller fragments to illustrate mRNA decay.](https://proteiniq.io/_next/image?url=%2Fimages%2Fguides%2Fhow-long-does-mrna-last-in-a-cell%2Ffeatured.webp&w=1920&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) Genetics · 11 min ### How long does mRNA last in a cell? Most mRNAs in mammalian cells have half-lives of a few hours, and bacterial mRNAs last about 5 minutes. See medians by organism and method, the shortest- and longest-lived transcripts, and how long vaccine mRNA stays detectable.](https://proteiniq.io/guides/how-long-does-mrna-last-in-a-cell)
- [![Ink illustration of one DNA gene region giving rise to different RNA transcripts.](https://proteiniq.io/_next/image?url=%2Fimages%2Fguides%2Fhuman-transcriptome-size%2Ffeatured.webp&w=1920&q=75&dpl=dpl_J6UAcmgysjTesCdwm3gj48dyXUyY) Genetics · 4 min ### How many transcripts are in the human transcriptome? The current human reference annotation contains 644,292 transcript models, 278,455 of them protein-coding. Database records, expressed isoforms and RNA molecules are different counts.](https://proteiniq.io/guides/human-transcriptome-size)

[See all guides](https://proteiniq.io/guides)

## Ready to discover RNA?

### Free

$0

For trying and exploring

- 200 credits, then 100/mo
- 3 jobs per day
- Every tool and example result
- Up to 1,000 residues per job
- SketchIQ, PDB and MSA viewers
- Academic license

[Get Free](https://proteiniq.io/sign-up)

### Plus

$23 per user per month, billed annually

For academic research

- Everything in Free
- 24,000 credits/user/year
- No daily job limit
- Batch runs
- API and MCP access
- Read-only viewers

### Pro

Popular

$79 per user per month, billed annually

For commercial work

- Everything in Plus
- 96,000 credits/user/year
- Run workflows
- More parallel jobs
- Larger file storage
- Commercial license

### Enterprise

Custom

For large organizations

- Everything in Pro
- Custom credit allocation
- Shared seats and admin roles
- Single sign-on
- Invoices and purchase orders
- Security review

[Contact sales](https://proteiniq.io/contact)

[View all plans and compare features](https://proteiniq.io/pricing)

## Frequently asked questions

AI answers from our docs. No sign-in needed.

## More solutions

The same workspace, set up for other kinds of discovery.

- [Small molecule Screen, dock, and rank small molecules Explore](https://proteiniq.io/solutions/small-molecule)
- [Antibody engineering Antibodies, checked before synthesis Explore](https://proteiniq.io/solutions/antibody-engineering)
- [Peptide discovery Send only your best peptides to the lab Explore](https://proteiniq.io/solutions/peptide-discovery)
- [Enzyme engineering Know which enzyme variants to make Explore](https://proteiniq.io/solutions/enzyme-engineering)