Compiler

The Compiler automates plasmid design for antibody and protein expression.

What is the Compiler?

The Compiler generates complete expression constructs from amino acid sequences. Given a protein sequence, it automatically:

• Optimizes codons for the target host

• Predicts and adds signal peptides

• Selects appropriate vector backbones

• Assembles all required genetic elements

• Generates ready-to-order plasmid designs

Supported Molecule Types

Monoclonal Antibodies (mAbs)

Standard antibody formats:

• Heavy chain + Light chain

• IgG, IgA, IgM formats

• Different isotype variants

Bispecific Antibodies

Antibodies targeting two antigens:

• Knob-in-hole formats

• CrossMab designs

• Common bispecific architectures

Fusion Proteins

Protein fusions:

• Fc-fusions

• Albumin fusions

• Custom linker options

Multispecific Molecules

Complex formats:

• Trispecifics

• Multi-domain proteins

• Custom architectures

Running the Compiler

Input Requirements

1. Amino acid sequences: Protein sequences to express

2. Format selection: Molecule architecture

3. Expression system: Target host (CHO, HEK293, etc.)

Workflow

1. Create a new molecule or select existing

2. Enter amino acid sequences

3. Select molecule format

4. Configure expression parameters

5. Run the Compiler

6. Review generated constructs

Configuration Options

• Codon optimization: Target organism preferences

• Signal peptide: Auto-predict or specify

• Vector template: Select backbone

• Regulatory elements: Promoter, terminator choices

Compiler Components

Codon Optimization

The Compiler includes Asimov's proprietary codon optimizer:

• Optimized for mammalian expression

• Avoids problematic sequences

• Maintains optimal GC content

Signal Peptide Prediction

Automatic signal peptide selection:

• Predicts optimal secretion signals

• Based on sequence properties

• Uses validated peptide library

Vector Templates

Pre-configured expression vectors:

• Optimized for specific hosts

• Include selection markers

• Ready for manufacturing

Expert Rules

Built-in design rules from:

• Literature best practices

• Asimov internal expertise

• Validated configurations

Reviewing Output

Generated Constructs

The Compiler creates:

• Complete plasmid sequences

• Full annotations

• Linked parts

• Ready for simulation

Construct Groups

Multi-chain molecules generate grouped constructs:

• HC plasmid

• LC plasmid

• Linked as a molecule

Quality Checks

Review automated checks:

• Sequence validation

• Reading frame verification

• Signal peptide placement

• Restriction site analysis

Templates

Preferred Templates

Mark templates as preferred:

1. Open template construct

2. In Info panel, mark as preferred

3. Compiler prioritizes this template

Custom Templates

Create custom vector templates:

1. Design your backbone

2. Add template markers

3. Save as template

4. Use in Compiler runs

Best Practices

Input Quality

• Verify amino acid sequences

• Check for unusual residues

• Confirm sequence boundaries

Format Selection

• Choose the simplest format that meets needs

• Consider manufacturing requirements

• Account for downstream applications

Review Output

• Check generated sequences

• Verify annotations

• Run simulations on output

• Confirm vector elements

Next Steps

• Simulation — Predict expression

• Runs History — View past runs

• Creating Constructs — Manual design