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
Know which enzyme variants to make
Map conserved positions, predict kinetics, and score mutations so only the most promising variants reach the bench.
Sequence and family context
Search homologs, align related enzymes, and identify conserved or coevolving positions before selecting residues to engineer.
MMseqs2
Search and cluster protein or nucleotide sequences for homology discovery at large scale.
sequence-analysiscomparison+4
HMMER
Sensitive sequence homology search using profile hidden Markov models
sequence-analysiscomparison+2
MAFFT
Align protein or nucleotide sequences with selectable accuracy and speed trade-offs.
sequence-analysisalignment+5
pySCA
Identify co-evolving residue sectors in protein families using Statistical Coupling Analysis.
sequence-analysiscoevolution-analysis+3
Protein parameters
Calculate molecular weight, pI, extinction coefficients, composition, and sequence indices.
protein-analysisphysicochemical-properties+1Structure and active-site preparation
Predict or repair the enzyme structure and inspect pockets, protonation, and likely binding-site context.
Boltz-2
Predict biomolecular complex structures and binding affinities for proteins, ligands, DNA, and RNA.
protein-foldingstructure-prediction+5
PDBFixer
Fix PDB and mmCIF structures by adding missing atoms, residues, hydrogens, and solvent.
structure-analysisquality-validation+3
fpocket
Identify protein pockets and ligand binding sites with druggability scores.
structure-analysisprotein+2
PROPKA 3
Predict pKa values of ionizable groups in proteins based on 3D structure.
protein-analysisproperty-prediction+3
ScanNet
Predict protein binding sites using geometric deep learning on 3D structures.
interaction-predictiondeep-learning+3Activity and substrate review
Estimate kinetic parameters or cleavage context and examine compatible substrate or inhibitor poses before redesign.
CatPred
Predict enzyme kcat, Km and Ki from sequences and SMILES, with uncertainty.
protein-analysisproperty-prediction+3
DLKcat
Predict enzyme kcat values from protein sequences and substrate structures or names.
protein-analysisproperty-prediction+3
CleaveNet
Predict MMP cleavage z-scores, evaluate substrates, and generate conditional peptides.
protein-analysisai-powered+4
Peptide cutter
Map protease and chemical cleavage sites across protein sequences for proteomics experiment planning.
protein-analysisphysicochemical-properties+2
GNINA
Dock small molecules into proteins using CNN scoring and physics-based pose optimization.
protein-dockingaffinity-prediction+4
PLIP
Profile protein-ligand interactions from a PDB complex structure.
structure-analysisinteraction-prediction+5Variant 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
Scaffold enzyme active sites with atom-level control and ligand-aware protein design.
protein-designenzyme-design+3
LigandMPNN
Design protein sequences around ligands, metals, and nucleotides for enzyme engineering and binding-site optimization.
sequence-designenzyme-design+4
ProteinMPNN
Design amino acid sequences for protein backbones with fixed positions, amino acid biases, and sequence diversity controls.
proteinsequence-design+2
Boltz Sequence Redesign
Redesign chosen residues on a fixed protein structure.
protein-designsequence-design+2
ESM-C Mutation Scoring
Score amino acid substitutions with masked protein language models.
sequence-analysisai-powered+3
ProteusAI
Learn from measured fitness and prioritize protein variants.
protein-designprotein+2Stability and validation
Compare thermostability, sequence stability, solubility, and structural geometry before choosing variants for assays.
ThermoMPNN
Predict mutation ΔΔG values and identify stabilizing substitutions for protein engineering.
protein-analysisproperty-prediction+3
Protein stability prediction
Compare independently interpretable sequence properties related to protein stability.
protein-analysisphysicochemical-properties+2
NetSolP-1.0
Predict protein solubility and purification usability for E. coli expression systems
protein-analysisproperty-prediction+3
MolProbity
Validate protein structures with clashscore, Ramachandran, rotamer, and geometry checks.
structure-analysisquality-validation+4
Frequently asked questions
ProteinIQ supports the computational stages of enzyme engineering in one connected workspace. Researchers can annotate sequences, inspect substrate context, predict turnover or stability, model structures, and score variants while keeping every output tied to the enzyme candidate it describes. Begin with an enzyme sequence or structure and select a workflow for activity, stability, mutation, or substrate analysis. ProteinIQ returns the source tables, structures, scores, and files needed to compare candidates before experimental enzyme assays.
ProteinIQ supports enzyme engineering workflows for enzyme annotation, substrate context review, activity prediction, kcat-style scoring, mutation and stability screening, structure modeling, and inhibitor or substrate triage. The platform keeps upstream tool outputs available so enzyme decisions can be reviewed rather than treated as black-box results.
ProteinIQ enzyme tools commonly accept enzyme FASTA sequences, PDB structures, substrate SMILES, inhibitor libraries, mutation lists, and tabular inputs depending on the upstream method. Each workflow keeps the accepted input type tied to the tool that generates the activity, stability, or structure output.
Yes. ProteinIQ can compare enzyme variants with mutation, stability, solubility, structure, and activity-related outputs depending on the selected tools. The results are preserved as tables, structure files, logs, and other artifacts so candidate variants can be compared side by side.
ProteinIQ can run enzyme activity and kcat-oriented prediction tools when the required sequence, structure, or substrate inputs are available. These outputs are computational prioritization signals, so ProteinIQ presents the scores and input context for review rather than treating them as measured kinetic constants.
Yes. ProteinIQ can connect enzyme sequences or structures to design, mutation scoring, and stability prediction tools that help prioritize variants for testing. The platform keeps the redesigned sequences, mutation tables, stability scores, and structure evidence tied to the original enzyme context.
Yes. When an enzyme workflow includes compound context, ProteinIQ can help review substrate or inhibitor candidates with structure, docking, property, and ADMET-style evidence depending on the tools selected. These results support triage and experimental planning rather than replacing biochemical validation.
No. ProteinIQ provides computational enzyme engineering and prioritization evidence. Enzyme kinetics, activity, specificity, stability, expression, and substrate-scope claims still require experimental enzyme assays before they should be treated as validated results.
Yes. ProteinIQ enzyme workflows can export CSV score tables, sequence files, predicted or prepared structures, mutation outputs, docking or compound tables, logs, and upstream result artifacts depending on the tool. Exported files preserve the evidence needed for review outside ProteinIQ.
Start in ProteinIQ with an enzyme sequence or structure and choose either a workflow template or a specific tool for activity prediction, stability review, structure modeling, or compound triage. Running a small test input first is the best way to confirm formatting before scaling to larger variant sets.
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