Modality Editor Reference

Supported Modalities

BioinvestGPT recognizes a full spectrum of therapeutic modalities. When you paste a SMILES string, an amino-acid sequence, a VH|VL chain pair, an ADC JSON payload, or an oligonucleotide sequence into the Seed Drug Input, the platform auto-detects the modality and opens the matching structure-aware editor. You can always override the detection from the modality dropdown.

The detector classifies into the modalities below. Most modalities feed a dedicated set of design levers; five of them also have a full visual structure editor (documented in the sections that follow): Small Molecule, Peptide, Antibody, ADC, and Oligonucleotide.

An Other / Unknown fallback also exists for custom or unclassified inputs — it accepts free-form structure text but does not open a visual editor.

Small Molecule Editor (Ketcher + RDKit)

The small-molecule editor pairs the Ketcher 2D drawing canvas with a live RDKit property dashboard. It is also the canvas used for PROTAC / degrader designs.

1

Draw or paste your structure

The Ketcher 2D canvas lets you draw molecular structures or paste SMILES notation. The RDKit dashboard on the right calculates properties in real time and scores them against the Lipinski Rule of 5:

Property	Lipinski Target	What It Means
Molecular Weight	< 500 Da	Larger molecules have poorer absorption
LogP	< 5	Lipophilicity affects distribution
H-Bond Donors	≤ 5	Affects membrane permeability
H-Bond Acceptors	≤ 10	Affects membrane permeability
TPSA	< 140 Ų	Polar surface area; < 90 for CNS
Rotatable Bonds	< 10	Flexibility affects bioavailability

Green checkmarks mean the property passes the rule. A red X marks a violation.

Tip: For CNS-targeted programs, watch TPSA closely — aim below 90 Ų rather than the general 140 Ų cutoff to favor blood-brain-barrier penetration.

The RDKit numbers are recomputed on every edit, so iterative structure-activity work (SAR) is immediate: change a substituent, watch MW / LogP / TPSA move, and keep your design inside the developability envelope before you commit it to a BVCT.

Peptide Bead Editor

Peptides (2–50 amino acids, linear or cyclic) open in the bead-on-string editor, where each residue is a colored bead you can click to modify.

2

Design peptide sequences

The bead-on-string editor displays each amino acid as a colored bead. Click any bead to:

• Substitute with a different amino acid (standard or non-natural)
• Toggle D-form, N-methylation, staple anchor, PEG site, or lipidation

Non-natural amino acids (Aib, Nal, pGlu, etc.) are shown with special modification icons.

Tip: Staple anchors and N-methylation are the usual levers for improving proteolytic stability and membrane permeability of a cyclic peptide.

Antibody CDR Editor

Monoclonal antibodies, bispecifics, and nanobodies (VHH) all open in the CDR editor, which renders the variable-domain sequences with the six complementarity-determining regions color-coded for precise editing.

3

Edit CDR regions

The CDR editor displays the VH (heavy) and VL (light) chain sequences with the 6 CDR regions color-coded:

Region	Color	Positions (Kabat)
CDR-H1	Pink	26–35
CDR-H2	Purple	50–65
CDR-H3	Blue	95–102
CDR-L1	Amber	24–34
CDR-L2	Emerald	50–56
CDR-L3	Orange	89–97

Click any CDR label to select and edit that region. UniProt-style index markers appear every 10 residues.

Tip: CDR-H3 is the most diverse loop and usually drives binding specificity — edit it first when re-engineering affinity.

Beyond the variable loops, the editor exposes Fc engineering presets that change effector function and half-life:

ADC Editor

Antibody-drug conjugates — and the ADC-adjacent formats AOC / ARC / PDC / RDC — open in the ADC editor, which combines the antibody scaffold with a linker/payload configuration panel.

4

Assemble antibody-drug conjugates

The ADC editor has two sections: the antibody section (the same VH/VL editor used for mAbs) and the linker/payload section (chemical-formula display). Configure the Drug-to-Antibody Ratio (DAR), the linker type (cleavable vs non-cleavable), and the payload molecule.

Oligonucleotide Editor

Antisense oligonucleotides (ASOs), siRNA, and miRNA therapeutics open in the oligonucleotide editor, where you set per-position chemistry, backbone linkages, and a delivery conjugation.

5

Design oligo modifications

Enter your base sequence (A, C, G, U, T), then click each position to select a sugar modification (2'-MOE, 2'-F, 2'-OMe, LNA). Toggle phosphorothioate (PS) backbone linkages per position, and choose a delivery conjugation.