Protein Engineering Service

Service Code: EG-SVC-PROT-ENG
Custom-scoped service — pricing by quotation
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Service Description
ServiceProtein Engineering
OverviewAn integrated, sequence-centered engineering campaign for enzymes, recombinant proteins, antibodies, nanobodies, multispecific formats, and proteins intended for capped-mRNA expression. Each campaign is organized around a defined experimental objective—such as soluble expression, stability, activity retention, interface design, developability, or binder generation—rather than a generic score.
Typical inputsExact amino-acid and, when available, coding FASTA sequences; experimental or predicted structures; expression host and construct context; known functional residues, interfaces, catalytic geometry, ligand context, DNA-contact footprints, or epitopes; benchmark/control proteins; prior expression and assay results; and explicit residues or regions that must remain unchanged.
Diagnostic workflowSequence and structure QC can examine identity and residue validity, hydrophobicity, charge, aggregation-prone regions, solubility features, cysteine burden, disorder, solvent exposure, surface hydrophobic patches, buried polar or charged residues, catalytic/contact geometry, construct context, and immunogenicity-related peptide windows. Where possible, matched functional or expression controls separate target-specific liabilities from vector, tag, host, and assay effects.
Design tracks
  • Solubility/expression: surface-patch removal, hydrophilic or supercharging substitutions, aggregation gatekeepers, NetSolP- or CamSol/AGGRESCAN-style evidence, consensus/stability-guided substitutions, construct review, and coding-sequence QC.
  • Stability/function: ESM-family and rational proposals constrained around catalytic, ligand-binding, structural, DNA-contact, or interface requirements, with optional ProteinMPNN/SolubleMPNN, ThermoMPNN, AntiFold, OpenMM, or other gated evidence.
  • Active-site/interface design: available LigandMPNN, PLACER, structure-provider, physical-ensemble, and specificity-control adapters, with exact redesigned and protected residues declared.
  • Antibodies and binders: CDR/Vernier/interface-protected humanization matrix, structure-aware sequence design, VHH redesign, de novo binder triage, and exact bispecific topology/chain validation.
  • mRNA-enabled research: protein and nucleotide construct review for transient capped-IVT-mRNA expression, with exact translation, codon/RNA QC, and manufacturing assumptions declared.
Algorithm matrixThe campaign selects from implemented native capabilities and approved adapters according to the biological question. Sequence, structure, complex, inverse-folding, physical, immunogenicity, and measured-data evidence remain in separate columns with applicability domains and abstentions. An adapter or catalog entry is not treated as installed or commercially cleared: executable, model-weight, database, sequence-transfer, and license checks occur before every run, and unavailable analyses are reported rather than silently substituted.
DeliverablesA problem-definition and constraint contract; validated parent and candidate protein and/or nucleotide FASTA; baseline diagnostics; exact mutation and construct maps; ranked, diversity-aware sequence panel; method-specific score and uncertainty matrix; structural models and visualizations where supported; experimental controls and testing recommendations; and a reproducible provenance package with input/output hashes, code/model/weight/data versions, parameters, and decision rationale in NextELN.
Privacy & traceabilityProprietary sequences can be processed through Excellgen's data-sovereign workflow with controlled GPU execution. NextELN keeps exact inputs, measurements, computational artifacts, provenance, human review, rejected candidates, and go/no-go decisions together.
Scientific boundaryAll designed sequences are hypotheses until tested. Structure confidence, solubility or expression models, language-model likelihood, interface metrics, docking, and computed-energy rankings are triage evidence—not proof of expression, folding, stability, activity, affinity, specificity, immunogenicity, safety, or therapeutic performance. Final claims require fit-for-purpose expression titre, SEC monomer/HMW, thermal stability, binding, specificity, and functional measurements.
EngagementExplore the scientific workspace at NextELN.com. Project scope depends on the target, exact sequence and construct context, available data, required design depth, GPU workload, and prospective validation plan. Contact Excellgen for a technical consultation and quotation.
Service Documents
DatasheetEG-SVC-PROT-ENG Product Datasheet
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