# Know which enzyme variants to make

Map conserved positions, predict kinetics, and score mutations so only the most promising variants reach the bench.

[Try it free](https://proteiniq.io/app/workflows/templates?template=enzyme-inhibitor-discovery)[Browse tools](https://proteiniq.io/app/tools)

![HIV-1 protease with darunavir, a Chai-1 result on ProteinIQ](https://proteiniq.io/_next/image?url=%2Fimages%2Fsolutions%2Fheroes%2Fenzyme-engineering.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9)

1. ## Sequence and family context

   Search homologs, align related enzymes, and identify conserved or coevolving positions before selecting residues to engineer.

   [![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)[![HMMER](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fhmmer.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### HMMER Sensitive sequence homology search using profile hidden Markov models sequence-analysiscomparison+2](https://proteiniq.io/app/hmmer)[![MAFFT](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fmafft.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### MAFFT Align protein or nucleotide sequences with selectable accuracy and speed trade-offs. sequence-analysisalignment+5](https://proteiniq.io/app/mafft)[![pySCA](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fpysca.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### pySCA Identify co-evolving residue sectors in protein families using Statistical Coupling Analysis. sequence-analysiscoevolution-analysis+3](https://proteiniq.io/app/pysca)[![Protein parameters](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fprotein-parameters.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Protein parameters Calculate molecular weight, pI, extinction coefficients, composition, and sequence indices. protein-analysisphysicochemical-properties+1](https://proteiniq.io/app/protein-parameters)
2. ## Structure and active-site preparation

   Predict or repair the enzyme structure and inspect pockets, protonation, and likely binding-site context.

   [![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)[![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)[![fpocket](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Ffpocket.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### fpocket Identify protein pockets and ligand binding sites with druggability scores. structure-analysisprotein+2](https://proteiniq.io/app/fpocket)[![PROPKA 3](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fpropka-3.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### PROPKA 3 Predict pKa values of ionizable groups in proteins based on 3D structure. protein-analysisproperty-prediction+3](https://proteiniq.io/app/propka)[![ScanNet](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fscannet.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ScanNet Predict protein binding sites using geometric deep learning on 3D structures. interaction-predictiondeep-learning+3](https://proteiniq.io/app/scannet)
3. ## Activity and substrate review

   Estimate kinetic parameters or cleavage context and examine compatible substrate or inhibitor poses before redesign.

   [![CatPred](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fcatpred.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### CatPred Predict enzyme kcat, Km and Ki from sequences and SMILES, with uncertainty. protein-analysisproperty-prediction+3](https://proteiniq.io/app/catpred)[![DLKcat](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fdlkcat.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### DLKcat Predict enzyme kcat values from protein sequences and substrate structures or names. protein-analysisproperty-prediction+3](https://proteiniq.io/app/dlkcat)[![CleaveNet](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fcleavenet.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### CleaveNet Predict MMP cleavage z-scores, evaluate substrates, and generate conditional peptides. protein-analysisai-powered+4](https://proteiniq.io/app/cleavenet)[![Peptide cutter](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fpeptide-cutter.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### Peptide cutter Map protease and chemical cleavage sites across protein sequences for proteomics experiment planning. protein-analysisphysicochemical-properties+2](https://proteiniq.io/app/peptide-cutter)[![GNINA](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fgnina.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### GNINA Dock small molecules into proteins using CNN scoring and physics-based pose optimization. protein-dockingaffinity-prediction+4](https://proteiniq.io/app/gnina)[![PLIP](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fplip.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### PLIP Profile protein-ligand interactions from a PDB complex structure. structure-analysisinteraction-prediction+5](https://proteiniq.io/app/plip)
4. ## Variant and scaffold design

   Generate new scaffolds, redesign sequences around structural and ligand-aware constraints, and prioritize variants from mutation scores or measured fitness.

   [![RFdiffusion 2](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Frfdiffusion2.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### RFdiffusion 2 Scaffold enzyme active sites with atom-level control and ligand-aware protein design. protein-designenzyme-design+3](https://proteiniq.io/app/rfdiffusion-2)[![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)[![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)[![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)[![ESM-C Mutation Scoring](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fesm-c-mutation-scoring.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ESM-C Mutation Scoring Score amino acid substitutions with masked protein language models. sequence-analysisai-powered+3](https://proteiniq.io/app/esm-c-mutation-scoring)[![ProteusAI](https://proteiniq.io/_next/image?url=%2Fimages%2Ftools%2Fproteusai.webp&w=1920&q=75&dpl=dpl_FAgf5acUWMGh21MEL7khBNAj8AH9) ### ProteusAI Learn from measured fitness and prioritize protein variants. protein-designprotein+2](https://proteiniq.io/app/proteusai)
5. ## Stability and validation

   Compare thermostability, sequence stability, solubility, and structural geometry before choosing variants for assays.

   [![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)[![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)

## Ready to engineer enzymes?

### Free

$0

The perfect starting place for your first project.

- All tools
- 200 credits, then 100/mo
- 3 jobs per day
- Up to 1,000 residues per job
- Academic license

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

### Plus

$23 per user/month

Everything an academic lab needs to scale.

- Everything in Free
- 24,000 credits/user/year
- No daily job limit
- Batches & workflows
- API access

### Pro

Popular

$79 per user/month

More compute and a commercial license for industry.

- Everything in Plus
- 96,000 credits/user/year
- Commercial license

### Enterprise

Contact us Custom annual terms

Custom credits, seats, and security review.

- Everything in Pro
- Custom credit allocation
- Shared seats and admin controls
- Invoice billing and 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.