Each model solves a distinct problem in computational biology — built from scratch, without borrowing pretrained encoders or inheriting the wrong inductive biases.
The first open foundation model for binding prediction across all five molecular modalities — protein, RNA, DNA, small molecule — built entirely from scratch. One universal atom representation. Shared encoder weights. No pretrained encoders borrowed.
A protein carbon and an RNA carbon pass through identical learned transformations. This is not a design constraint — it is the entire point.
X-modal Unified Zero-shot Universal aptamer language model for de novo DNA and RNA aptamer design against any protein target — no SELEX experimental data required.
Powered by FEBI (Fundamental Encoding Block Intelligence) and RJ (Relational Junction) — proprietary blocks for sequence context and structural graph propagation. A built-in GER loop refines generation via REINFORCE toward lower Kd.
RNA 3D structure prediction model — codenamed RNX during development and competition. Competed in the Stanford RNA 3D Folding Part 2 Kaggle challenge, placing 89th out of 1,867 teams worldwide, earning a Silver Medal — awarded March 26, 2026.
RNJ is the structural counterpart to XUZU: where XUZU uses dot-bracket secondary structure as input context, RNJ predicts the full 3D atomic coordinates that define RNA tertiary fold and binding geometry.
| System | Modalities | Affinity | Structure | Generation | Aptamers | Open |
|---|---|---|---|---|---|---|
| BindFM | All 5 | ✓ | ✓ | ✓ | ✓ modified | ✓ |
| AlphaFold3 | Protein+SM+NA | ✗ | ✓ | ✗ | partial | ✗ |
| Boltz-2 | Protein+SM | ✓ | ✓ | ✗ | ✗ | ✓ |
| DiffDock | Protein+SM | ✗ | ✓ | ✗ | ✗ | ✓ |
| AptaBLE | Aptamer+Protein | partial | ✗ | ✗ | ✓ | ✓ |
| RoseTTAFold-AA | Protein+SM+NA | ✗ | ✓ | ✗ | partial | ✓ |
BindFM's shared-weight EGNN encoder ensures a protein carbon and an RNA carbon live in the same representation space — making cross-modality binding interactions mathematically comparable, not just empirically correlated.
Every serious attempt at universal binding prediction hits the same wall: incompatible representation spaces. BindFM takes the only principled approach — represent every molecular entity as the same thing it actually is: a graph of atoms in 3D space.
— Hamza Abdullah, terminalBio
terminalBio is a BioAI startup building the foundational layer for molecular intelligence — open models that treat every atom, sequence, and structure as part of Unified TB Biocompute: the OS for synthetic biology.
Where most AI biology tools fragment the problem, terminalBio builds one model that speaks all modalities. The same encoder. The same weights. One representation space — because at the atomic level, biology is one problem.