# Will your design actually fold?

Generate backbones and binders, design their sequences, and fold them with independent models before you order genes.

[Try it free](https://proteiniq.io/app/workflows/templates?template=protein-design-stability-screen)[Browse tools](https://proteiniq.io/app/tools)

![De novo protein design, a RFdiffusion3 result on ProteinIQ](https://proteiniq.io/_next/image?url=%2Fimages%2Fsolutions%2Fheroes%2Fprotein-engineering.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9)

1. ## Backbone and binder generation

   Generate candidate backbones or target-conditioned binders from the structural constraints that define the design problem.

   [![RFdiffusion3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Frfdiffusion3.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### RFdiffusion3 All-atom generative diffusion for designing binders, enzymes, and symmetric protein assemblies protein-designenzyme-design+3](https://proteiniq.io/app/rfdiffusion3)[![RFdiffusion](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Frfdiffusion.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### RFdiffusion Design protein structures for de novo scaffolds, binders, motifs, and symmetric oligomers. protein-designdiffusion-model+2](https://proteiniq.io/app/rfdiffusion)[![BindCraft](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fbindcraft.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### BindCraft Design de novo protein binders for target surfaces using structure-guided sequence generation. binder-designai-powered+3](https://proteiniq.io/app/bindcraft)[![FreeBindCraft](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fbindcraft.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### FreeBindCraft Design de novo protein binders for target surfaces using structure-guided sequence generation. binder-designai-powered+3](https://proteiniq.io/app/freebindcraft)[![BoltzProt-1](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fboltzprot-1.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### BoltzProt-1 Protein, peptide, nanobody and antibody binder design. protein-designbinder-design+3](https://proteiniq.io/app/boltzprot-1)[![ESMFold2 Binder Design](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fesmfold2-binder-design.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ESMFold2 Binder Design Design minibinders and antibody scFvs against a protein target. binder-designai-powered+2](https://proteiniq.io/app/esmfold2-binder-design)
2. ## Sequence design and redesign

   Assign sequences to designed structures or conformational ensembles, or redesign chosen residues around ligand and solubility constraints.

   [![ProteinMPNN](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2FproteinMPNN-featured.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ProteinMPNN Design amino acid sequences for protein backbones with fixed positions, amino acid biases, and sequence diversity controls. proteinsequence-design+2](https://proteiniq.io/app/protein-mpnn)[![LigandMPNN](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fligand-mpnn-featured.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### LigandMPNN Design protein sequences around ligands, metals, and nucleotides for enzyme engineering and binding-site optimization. sequence-designenzyme-design+4](https://proteiniq.io/app/ligand-mpnn)[![SolubleMPNN](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fsolublempnn.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### SolubleMPNN Design sequences with the ProteinMPNN-family model trained on structures from soluble-protein PDB IDs. proteinsequence-design+2](https://proteiniq.io/app/soluble-mpnn)[![ESM-IF1](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fesm-if1.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ESM-IF1 Design protein sequences from 3D backbone structures with controllable sampling diversity. sequence-designdeep-learning+2](https://proteiniq.io/app/esm-if1)[![Caliby](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fcaliby.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Caliby Design sequences for a structure or an aligned ensemble proteinsequence-design+1](https://proteiniq.io/app/caliby)[![Boltz Sequence Redesign](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fboltz-sequence-redesign.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Boltz Sequence Redesign Redesign chosen residues on a fixed protein structure. protein-designsequence-design+2](https://proteiniq.io/app/boltz-sequence-redesign)
3. ## Structure prediction

   Fold candidate sequences with independent models and compare confidence instead of relying on the design model alone.

   [![AlphaFold2](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Falphafold-2.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### AlphaFold2 Predict protein structures and complexes with single-sequence or MSA-assisted folding. protein-foldingstructure-prediction+4](https://proteiniq.io/app/alphafold-2)[![ESMfold](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fesmfold.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ESMfold Predict protein structures and multimers directly from sequences without an MSA. protein-foldingstructure-prediction+2](https://proteiniq.io/app/esmfold)[![Boltz-2](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fboltz-2.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Boltz-2 Predict biomolecular complex structures and binding affinities for proteins, ligands, DNA, and RNA. protein-foldingstructure-prediction+5](https://proteiniq.io/app/boltz-2)[![Chai-1](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fchai-1.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Chai-1 Predict 3D structures for proteins, ligands, DNA, RNA, and multi-component complexes. protein-foldingstructure-prediction+5](https://proteiniq.io/app/chai-1)[![OpenFold-3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fopenfold-3.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### OpenFold-3 Open-source AlphaFold3-based structure prediction for proteins, ligands, DNA, and RNA protein-foldingstructure-prediction+5](https://proteiniq.io/app/openfold-3)[![RosettaFold3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Frosettafold3.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### RosettaFold3 Open-source structure prediction for proteins, nucleic acids, and ligands protein-foldingstructure-prediction+5](https://proteiniq.io/app/rosettafold3)
4. ## Stability and developability review

   Review thermostability, sequence stability, solubility, aggregation, and surface exposure before selecting designs.

   [![ThermoMPNN](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fthermompnn.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ThermoMPNN Predict mutation ΔΔG values and identify stabilizing substitutions for protein engineering. protein-analysisproperty-prediction+3](https://proteiniq.io/app/thermompnn)[![Protein stability prediction](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fprotein-stability.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Protein stability prediction Compare independently interpretable sequence properties related to protein stability. protein-analysisphysicochemical-properties+2](https://proteiniq.io/app/protein-stability)[![NetSolP-1.0](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fnetsolp.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### NetSolP-1.0 Predict protein solubility and purification usability for E. coli expression systems protein-analysisproperty-prediction+3](https://proteiniq.io/app/netsolp-1-0)[![Aggrescan3D](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Faggrescan3d.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Aggrescan3D Analyze aggregation-prone regions in a protein structure. protein-analysisproperty-prediction+3](https://proteiniq.io/app/aggrescan3d)[![SASA calculator](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fsasa-calculator.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### SASA calculator Calculate solvent accessible surface area for protein structures structure-analysisprotein+1](https://proteiniq.io/app/sasa-calculator)
5. ## Structural validation and comparison

   Repair models, validate geometry, score predicted interfaces, and compare folds and family context before experimental review.

   [![PDBFixer](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fpdb-fixer-featured.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### PDBFixer Fix PDB and mmCIF structures by adding missing atoms, residues, hydrogens, and solvent. structure-analysisquality-validation+3](https://proteiniq.io/app/pdb-fixer)[![MolProbity](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fmolprobity.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### MolProbity Validate protein structures with clashscore, Ramachandran, rotamer, and geometry checks. structure-analysisquality-validation+4](https://proteiniq.io/app/molprobity)[![IPSAE](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fipsae.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### IPSAE Score interprotein interactions in AlphaFold and Boltz predictions structure-analysisquality-validation+2](https://proteiniq.io/app/ipsae)[![FoldSeek](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Ffoldseek.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### FoldSeek Search AlphaFold DB, compare structures, or cluster by 3D similarity structure-analysisalignment+3](https://proteiniq.io/app/foldseek)[![USAlign](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fusalign.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### USAlign Universal structure alignment for proteins, RNA, and DNA molecules structure-analysisalignment+4](https://proteiniq.io/app/usalign)[![MMseqs2](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fmmseqs2.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### MMseqs2 Search and cluster protein or nucleotide sequences for homology discovery at large scale. sequence-analysiscomparison+4](https://proteiniq.io/app/mmseqs2)

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