01
Biology comes first.
Start with meaningful scientific questions. Let the biological problem guide the work.
Molecular Animation v0.3.0 is open source
Agentic AI for biological research.
AmadeusBio.ai is developing research systems to tackle complex biological challenges, and building open-source tools that help scientists see molecular mechanisms clearly and honestly.
01 Molecular Animation
Molecular films that are both beautiful and honest.
Our open framework turns a scientific brief into a Blender film built from PDB structures. Labels on screen state whether each beat shows experimental structure or an illustrative step.
A 21-second silent film of channelrhodopsin C1C2, built from PDB structures 9GO1 and 9GO2. It opens on the protein dimer in a lipid membrane as photons arrive, dives into the retinal pocket, and shows retinal twisting from all-trans to 13-cis (an illustrative morph between the two crystal states). Lys132 then swings toward Glu129 to form a salt bridge. A section through the cation pathway first shows it interrupted, as in the crystal, then open in an illustrative conducting-state model as sodium ions cross the membrane. Throughout, lipids, side chains and the protein move with illustrative thermal motion at literature rates, one second of film standing for about a nanosecond.
On screen, beat by beatCase study · Channelrhodopsin C1C2 · PDB 9GO1 / 9GO2
- 0:00Channelrhodopsin C1C2Light-gated cation channel (ChR1/ChR2 chimera) in a membraneExperimental1 s of film ≈ 1 ns
- 0:04Retinal, the light sensorCovalently bound to Lys296 inside each protomerExperimental1 s of film ≈ 1 ns
- 0:07A photon twists retinalAll-trans → 13-cis about the C13=C14 bondIllustrativewithin a picosecond
- 0:10The protein respondsLys132 swings to Glu129 and forms a salt bridgeExperimentalmicroseconds
- 0:15The pathway is still interruptedIn this early light-activated state the gates stay narrowExperimental1 s of film ≈ 1 ns
- 0:17Open channel: cations cross the membraneConducting state shown as an illustrative modelIllustrativemilliseconds
2,316 / 2,321
heavy atoms per protomer matched between the dark and light crystal states
494k
lipid atoms in a procedural membrane
≥ 1.75 Å
minimum gap from every ion centre to the nearest atom surface
1/255
posters reproduced within this tolerance after a refactor
02 Approach
Designed around scientific questions.
Our aim is to develop AI systems for connected research problems, rather than isolated tasks. A biological question rarely stands alone: it leads to further questions, invites different perspectives, and changes as the evidence develops.
We are interested in how computational tools can contribute to that process and to deeper biological understanding.
Our approach03 Working principles
Scientific ambition. Careful judgment.
Biological relevance, careful evaluation, and clear communication of uncertainty guide the work we aim to do.
02
Evaluate with care.
Examine what a system can do, where it falls short, and what the evidence supports.
03
Make uncertainty clear.
Distinguish an observation from an interpretation, and a promising direction from a demonstrated result.
04 Our work
What we are building.
Research systems that are still in development, and open tools we release when they are ready to be useful to others.
Illustration
In development
Agentic research systems
AI that can support the process of scientific investigation: working across connected questions rather than isolated tasks.
Antibody · PDB 1IGT
Released · v0.3.0
Molecular Animation
An open framework for turning a scientific brief into an honest, beautiful molecular film with Blender, designed to be driven by an AI agent and to work just as well by hand.
Contact
Start a conversation.
For research collaborations, molecular animation, partnerships and press, we would be glad to hear from you.
Nucleosome (PDB 1KX5). The histone spool’s surface is coloured by its Coulombic potential, blue positive; the DNA, drawn atom by atom, carries one negative charge on each of its 292 phosphate groups, in red.