Open Research Lab · Computational Biology

Every atom.
One language. Always open.

Building open foundation models for computational biology — where every atom, sequence, and structure speaks the same language. No pretrained encoders borrowed. No compromises made.

3
Foundation Models
5
Modalities
89th
Global Rank

Three models.
One physics.

Each model solves a distinct problem in computational biology — built from scratch, without borrowing pretrained encoders or inheriting the wrong inductive biases.

BindFM
Universal Binding Foundation Model
Foundation Model MIT License v0.1

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.

EGNN Encoder PairFormer Trunk OT-CFM Flow Matching 197-dim Atom Tokens ~380M params 4-Stage Curriculum
Binding Modalities
01
Protein ↔ Small Molecule
Drug-target, covalent inhibitors
02
Protein ↔ Protein
PPI, antibody-antigen, SKEMPI2
03
Protein ↔ Nucleic Acid
RBPs, CRISPR-Cas9, splicing
04
Nucleic ↔ Small Molecule
Aptamer-drug, riboswitches
05
Nucleic ↔ Nucleic
siRNA-mRNA, aptamer secondary structure, miRNA targeting
~380MFull params
4 StagesCurriculum
9Benchmarks
~40 minColab run
XUZU
Multi-Modal Aptamer Language Model
v1.0.0 Released

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.

FEBI Blocks RJ Graph Attn D3PM Decoder ~7.5M params GER Refinement
~7.5MParameters
14Token types
100TDiffusion steps
RNJ
RNA 3D Structure Prediction Model
🥈 Silver Medal Kaggle

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.

3D Coordinates Tertiary Structure Codename: RNX 1,867 Teams
Kaggle Silver Medal Certificate — Stanford RNA 3D Folding Part 2, Hamza A, 89th of 1867 teams, March 26 2026
89thGlobal Rank
1,867Teams
🥈 SilverMedal
Mar 2026Awarded

Where we stand.
Honestly.

System Modalities Affinity Structure Generation Aptamers Open
BindFMAll 5 ✓ modified
AlphaFold3Protein+SM+NApartial
Boltz-2Protein+SM
DiffDockProtein+SM
AptaBLEAptamer+Proteinpartial
RoseTTAFold-AAProtein+SM+NApartial

One encoder.
Every molecule.

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.

Shared EGNN Encoder — SE(3)-equivariant. Same weights process both binding partners in parallel.
PairFormer Trunk — 32 layers of triangle attention + outer product mean, adapted from AlphaFold2.
Three Co-trained Heads — Affinity (Kd, kon/koff, t½), Structure (3D coordinates), Generative (de novo binders).
XUZU's FEBI + RJ — Proprietary transformer and graph attention blocks for aptamer-specific multi-modal encoding with GER self-refinement.
XUZU Inference Pipeline
NucleotideLanguageEncoder
FEBI × 6 · RoPE Attention
StructureGraphEncoder
RJ × 3 · Base-pair Graph
TargetProteinEncoder
FEBI × 3 · Pocket AA Seq
CrossModalFusion
3-way Softmax Gate
DiscreteDiffusionDecoder
D3PM · 100 Timesteps
Aptamer
↺ GER Loop · REINFORCE toward lower Kd · Iterative self-refinement
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

Built from
first principles.

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.

Full story →
01
No borrowed encoders
Every model is built from scratch. Inheriting evolutionary language model representations introduces the wrong inductive biases at every modality boundary crossing.
02
One representation space
A protein carbon and an RNA carbon are both carbons. They should live in the same learned embedding space — and in BindFM, they do.
03
Always open
All models released under MIT license. Science advances by building on prior work — that only works if the work is actually accessible.
# terminalBio · Universal Binding Prediction
from terminalbio import BindFM, XUZU

# Load universal binding model
model = BindFM.from_pretrained("terminalbio/bindfm-v0.1")

# Predict affinity across modalities
result = model.predict(
  partner_a="MKTIIALSYIFCLVFA...",  # protein
  partner_b="GGGACCCUGCUUUCG...",  # RNA aptamer
  task="affinity"
)

# → Kd: 12.4 nM | ΔG: -10.8 kcal/mol
print(result.kd)   # 1.24e-8

# Design aptamers with XUZU
aptamer = XUZU.design(
  target="KPC-2 beta-lactamase",
  modality="RNA",
  n_candidates=100
)