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We engineer biomolecules and use explainable virtual cells to accurately forecast pre-clinical success.
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Joined December 2024
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Today, we are incredibly excited to present LiteMol-1, our very first foundation model from LiteFold.
Structure-based models like BoltzGen, O-Design, and RFdiffusion have become the de facto standard for designing biomolecules. However, they are expensive to run at scale. In many campaigns, we have to generate tens of thousands of designs and rigorously filter them down to a handful of top candidates.
More importantly, most molecule design systems are primarily optimized around binding. But what about everything else that makes a molecule a useful therapeutic: ADME, toxicity, drug-likeness, membrane permeability, synthesizability, selectivity, and more?
That’s where we introduce LiteMol-1, our first Multi-Molecule Foundation Diffusion Language Model, pre-trained from scratch. With a single set of weights, LiteMol-1 can conditionally generate small molecules, peptides, cyclic peptides, depsipeptides, peptides with ncAAs, macrocycles, and PROTACs.
You can generate molecules unconditionally or condition generation on a protein target sequence. You can in-paint molecules, preserve parts of an existing scaffold, generate non-canonical peptides, cyclize designs, and continuously edit and regenerate them.
We also introduce a Monte Carlo Tree Search framework for multi-objective molecular design. Instead of trying to make one molecule perfect at everything, the search keeps a set of promising molecules, each with different trade-offs across properties. This matters because molecular design is fundamentally not a single-objective optimization problem.
Finally, and probably the part we are most excited about: this is a model for Agents. LLMs are not particularly efficient interfaces for repeatedly reasoning over thousands of large PDB/CIF files inside an AutoResearch loop. Sequence space is different. SMILES and molecular sequences are compact, editable, and much easier for an agent to inspect, compare, modify, and reason over.
So we treat LiteMol-1 as an infinite molecular canvas.
The model generates possibilities. The agent takes inspiration from them, evaluates them, edits them, optimizes them, and generates again. The AutoResearch loop continues until it finds candidates that satisfy the given design objectives; while bringing in expensive structure prediction, docking, or simulation only when they are actually needed.
Our evaluations across peptide and small-molecule generation show that LiteMol-1 is competitive with, and in several settings on-par with or better than, frontier structure-based and sequence-based models, while operating at a fraction of the generation cost and time.
And this is only the first step. Check out our technical research blog post in the comments to learn more about LiteMol-1.
LiteFold retweeted
infra blog cuz making AI do science required reinventing distributed systems
Introducing Hybrid Scientific Intelligence Runtime.
In pharma and biotech, some of the most valuable data like: sequences, SAR tables, assay results, lab notebooks, internal reports cannot just be sent to an external AI provider. HSIR lets companies run models, agents, sandboxes, scientific workflows and governance inside infrastructure they already own, while still allowing controlled use of frontier models and cloud compute when the task actually needs them.
We also benchmarked the runtime. On the public DAX full-build benchmark, HSIR completed the workload in 55.8 seconds, ahead of Daytona, Vercel, Modal and Runloop among the providers we compared that completed the full workload.
The direction is straightforward: make scientific AI private where it needs to be, hybrid where it makes sense, and fast enough that teams do not have to choose between control and capability. Blogpost link in the comments.
LiteFold retweeted
We built a Modal-like infrastructure layer for scientific AI, but made the deployment medium agnostic.
The interface stays the same, but the actual compute can sit on-prem, inside a customer VPC across multiple environments. Underneath, HSIR brings together GPU/CPU workflows, agent sandboxes, LLM inference, agent orchestration, and governance as one runtime.
For pharma and biotech, this matters because the bottleneck is not just model capability. It is whether teams can actually own the infrastructure, keep sensitive data inside their boundary, and still use modern agentic workflows without stitching together five different systems.
That is why we built HSIR, the Hybrid Scientific Intelligence Runtime.
Same experience. Different execution environments. Customer owns the boundary. We wrote up how it works, where it runs, and the benchmarks in the release blog below.
Introducing Hybrid Scientific Intelligence Runtime.
In pharma and biotech, some of the most valuable data like: sequences, SAR tables, assay results, lab notebooks, internal reports cannot just be sent to an external AI provider. HSIR lets companies run models, agents, sandboxes, scientific workflows and governance inside infrastructure they already own, while still allowing controlled use of frontier models and cloud compute when the task actually needs them.
We also benchmarked the runtime. On the public DAX full-build benchmark, HSIR completed the workload in 55.8 seconds, ahead of Daytona, Vercel, Modal and Runloop among the providers we compared that completed the full workload.
The direction is straightforward: make scientific AI private where it needs to be, hybrid where it makes sense, and fast enough that teams do not have to choose between control and capability. Blogpost link in the comments.
LiteFold retweeted
Introducing Hybrid Scientific Intelligence Runtime.
In pharma and biotech, some of the most valuable data like: sequences, SAR tables, assay results, lab notebooks, internal reports cannot just be sent to an external AI provider. HSIR lets companies run models, agents, sandboxes, scientific workflows and governance inside infrastructure they already own, while still allowing controlled use of frontier models and cloud compute when the task actually needs them.
We also benchmarked the runtime. On the public DAX full-build benchmark, HSIR completed the workload in 55.8 seconds, ahead of Daytona, Vercel, Modal and Runloop among the providers we compared that completed the full workload.
The direction is straightforward: make scientific AI private where it needs to be, hybrid where it makes sense, and fast enough that teams do not have to choose between control and capability. Blogpost link in the comments.
Introducing Hybrid Scientific Intelligence Runtime.
In pharma and biotech, some of the most valuable data like: sequences, SAR tables, assay results, lab notebooks, internal reports cannot just be sent to an external AI provider. HSIR lets companies run models, agents, sandboxes, scientific workflows and governance inside infrastructure they already own, while still allowing controlled use of frontier models and cloud compute when the task actually needs them.
We also benchmarked the runtime. On the public DAX full-build benchmark, HSIR completed the workload in 55.8 seconds, ahead of Daytona, Vercel, Modal and Runloop among the providers we compared that completed the full workload.
The direction is straightforward: make scientific AI private where it needs to be, hybrid where it makes sense, and fast enough that teams do not have to choose between control and capability. Blogpost link in the comments.
Blogpost link: litefold.ai/blogs/hybrid-sci…
Reach us out if you want to deploy LiteFold for your scientific usecases.
LiteFold retweeted
This is crazy. We trained on over 100 million molecules, there's no shot this is memorized. It knows exactly what is needed to fit into the binding site. Virtual screening is over, dead on arrival.
I could simply add a scoring function that constrains generation to composable building blocks and then each molecule is guaranteed to be synthesizable from Enamine or whoever (and we are doing that right now).
LiteFold retweeted
Replying to @EliLillyandCo
@EliLillyandCo was right, every biotech should pull their targets publicly from their pipelines.
Our model LiteMol-1 model took one shot at their MALT1 target, and without any extra tuning only pocket conditioning, their pyrazolyl methyl-formamidopyridine just fell out. Yea there's some variations, and even some generations that recover even more of the original molecule.
But I ran this on an M1 Max MacBook, it took 30 seconds, and this is only the first run. I didn't even turn on most of the medchem objectives. I could keep mining away for another 10,000 molecules and comb the entire binding site. Most of these molecules score between -8 kcal/mol - -10 kcal/mol. I even had a -12 kcal/mol in the list.
LiteFold retweeted
And we got featured in the front page chat! Less goo! All Thanks to AIM to feature us! We have so much things to build and research from here on. Super Excited!
Links below
It was a pleasure speaking at @Analyticsindiam about @try_litefold .
We discussed about:
- The current landscape of AI x Bio
- Our first Foundation Model: Lite-Mol1
- What are the current pitfalls and where AI has still a long way to go
- Bit about disease understanding, forecasting preclinical properties and molecule design
- How the drug discovery and development would look in the coming 5 years
- The current landscape for India in Drug Development and where are the areas India has the edge
Amazing experience, and kudos to the team for hosting me. Do check out and let us know your thoughts!
youtu.be/MvXkE8Gw8uU?si=xZ6U…
LiteFold retweeted
Very happy to support young Indian entrepreneurs who are willing to take on global challenges which can make life better for all of us !
@anindyadeeps
@try_litefold
youtube.com/watch?v=MvXkE8Gw…
🚀🚀🚀
It was a pleasure speaking at @Analyticsindiam about @try_litefold .
We discussed about:
- The current landscape of AI x Bio
- Our first Foundation Model: Lite-Mol1
- What are the current pitfalls and where AI has still a long way to go
- Bit about disease understanding, forecasting preclinical properties and molecule design
- How the drug discovery and development would look in the coming 5 years
- The current landscape for India in Drug Development and where are the areas India has the edge
Amazing experience, and kudos to the team for hosting me. Do check out and let us know your thoughts!
youtu.be/MvXkE8Gw8uU?si=xZ6U…
LiteFold retweeted
It was a pleasure speaking at @Analyticsindiam about @try_litefold .
We discussed about:
- The current landscape of AI x Bio
- Our first Foundation Model: Lite-Mol1
- What are the current pitfalls and where AI has still a long way to go
- Bit about disease understanding, forecasting preclinical properties and molecule design
- How the drug discovery and development would look in the coming 5 years
- The current landscape for India in Drug Development and where are the areas India has the edge
Amazing experience, and kudos to the team for hosting me. Do check out and let us know your thoughts!
youtu.be/MvXkE8Gw8uU?si=xZ6U…
LiteFold retweeted
What we need next is new set of verifiers and better proxies
nitter.cf/try_litefold/status/20…
What we need next is new set of verifiers and better proxies
nitter.cf/try_litefold/status/20…
LiteFold retweeted
Love the shift from “best binder wins” to “best overall molecule survives.” Binding is the entry ticket, developability is the game. If LiteMol-1 + MCTS can cheaply explore the Pareto frontier (ADME/tox/synth/etc.) and only spend structure compute when it matters, that’s a real workflow unlock.
Today, we are incredibly excited to present LiteMol-1, our very first foundation model from LiteFold.
Structure-based models like BoltzGen, O-Design, and RFdiffusion have become the de facto standard for designing biomolecules. However, they are expensive to run at scale. In many campaigns, we have to generate tens of thousands of designs and rigorously filter them down to a handful of top candidates.
More importantly, most molecule design systems are primarily optimized around binding. But what about everything else that makes a molecule a useful therapeutic: ADME, toxicity, drug-likeness, membrane permeability, synthesizability, selectivity, and more?
That’s where we introduce LiteMol-1, our first Multi-Molecule Foundation Diffusion Language Model, pre-trained from scratch. With a single set of weights, LiteMol-1 can conditionally generate small molecules, peptides, cyclic peptides, depsipeptides, peptides with ncAAs, macrocycles, and PROTACs.
You can generate molecules unconditionally or condition generation on a protein target sequence. You can in-paint molecules, preserve parts of an existing scaffold, generate non-canonical peptides, cyclize designs, and continuously edit and regenerate them.
We also introduce a Monte Carlo Tree Search framework for multi-objective molecular design. Instead of trying to make one molecule perfect at everything, the search keeps a set of promising molecules, each with different trade-offs across properties. This matters because molecular design is fundamentally not a single-objective optimization problem.
Finally, and probably the part we are most excited about: this is a model for Agents. LLMs are not particularly efficient interfaces for repeatedly reasoning over thousands of large PDB/CIF files inside an AutoResearch loop. Sequence space is different. SMILES and molecular sequences are compact, editable, and much easier for an agent to inspect, compare, modify, and reason over.
So we treat LiteMol-1 as an infinite molecular canvas.
The model generates possibilities. The agent takes inspiration from them, evaluates them, edits them, optimizes them, and generates again. The AutoResearch loop continues until it finds candidates that satisfy the given design objectives; while bringing in expensive structure prediction, docking, or simulation only when they are actually needed.
Our evaluations across peptide and small-molecule generation show that LiteMol-1 is competitive with, and in several settings on-par with or better than, frontier structure-based and sequence-based models, while operating at a fraction of the generation cost and time.
And this is only the first step. Check out our technical research blog post in the comments to learn more about LiteMol-1.
LiteFold now wants to help researchers identify molecules with a realistic chance of pre-clinical success.
We wrote about LiteMol-1, wet-lab validation, collaboration between AI and biology teams, and the growing demand for research services in pharma.
Read more:
3f.vc/article/what-goes-into…
LiteFold retweeted
After going through the LiteMol-1 writeup, what really stuck with me wasn't just “AI generating molecules.”
It was the idea of making molecular design agent-native.
You give the agent a molecular sequence it can actually work with — generate something, inspect it, run evaluations, change parts of it, search through promising directions, and then try again.
generate → inspect → simulate → evaluate → edit → repeat.
At some point, this starts feeling less like a model that generates stuff and more like a building block for automated scientific research.
The MCTS + diffusion part is especially interesting to me. Instead of just generating a massive pile of molecules and filtering them afterward, the search can spend more compute exploring the candidates that actually look promising.
And I think that's the bigger idea here.
AI for science isn't only going to be about building bigger or better foundation models.
It's going to be about putting these models inside loops where they can come up with hypotheses, test them, learn from the results, and decide what to try next.
LiteMol-1 feels like a pretty interesting glimpse of that future.
It's still early, and these are computational results without wet-lab validation yet.
But honestly, the direction is fucking fascinating.
Big times ahead @anindyadeeps
Today, we are incredibly excited to present LiteMol-1, our very first foundation model from LiteFold.
Structure-based models like BoltzGen, O-Design, and RFdiffusion have become the de facto standard for designing biomolecules. However, they are expensive to run at scale. In many campaigns, we have to generate tens of thousands of designs and rigorously filter them down to a handful of top candidates.
More importantly, most molecule design systems are primarily optimized around binding. But what about everything else that makes a molecule a useful therapeutic: ADME, toxicity, drug-likeness, membrane permeability, synthesizability, selectivity, and more?
That’s where we introduce LiteMol-1, our first Multi-Molecule Foundation Diffusion Language Model, pre-trained from scratch. With a single set of weights, LiteMol-1 can conditionally generate small molecules, peptides, cyclic peptides, depsipeptides, peptides with ncAAs, macrocycles, and PROTACs.
You can generate molecules unconditionally or condition generation on a protein target sequence. You can in-paint molecules, preserve parts of an existing scaffold, generate non-canonical peptides, cyclize designs, and continuously edit and regenerate them.
We also introduce a Monte Carlo Tree Search framework for multi-objective molecular design. Instead of trying to make one molecule perfect at everything, the search keeps a set of promising molecules, each with different trade-offs across properties. This matters because molecular design is fundamentally not a single-objective optimization problem.
Finally, and probably the part we are most excited about: this is a model for Agents. LLMs are not particularly efficient interfaces for repeatedly reasoning over thousands of large PDB/CIF files inside an AutoResearch loop. Sequence space is different. SMILES and molecular sequences are compact, editable, and much easier for an agent to inspect, compare, modify, and reason over.
So we treat LiteMol-1 as an infinite molecular canvas.
The model generates possibilities. The agent takes inspiration from them, evaluates them, edits them, optimizes them, and generates again. The AutoResearch loop continues until it finds candidates that satisfy the given design objectives; while bringing in expensive structure prediction, docking, or simulation only when they are actually needed.
Our evaluations across peptide and small-molecule generation show that LiteMol-1 is competitive with, and in several settings on-par with or better than, frontier structure-based and sequence-based models, while operating at a fraction of the generation cost and time.
And this is only the first step. Check out our technical research blog post in the comments to learn more about LiteMol-1.
LiteFold retweeted
Great work! @try_litefold! Look forward to seeing what you guys do next.
Super proud and excited to finally present LiteMol-1. This is our first foundation model from LiteFold, pre-trained from scratch.
Today, LiteMol-1 can generate small molecules, peptides, cyclic peptides, depsipeptides, peptides with ncAAs, macrocycles, and PROTACs.
Across our peptide and small-molecule evaluations, the model shows competitive results. In several settings, we are on-par with or better than frontier structure-based models, at a fraction of the generation cost.
But the part I find most interesting is that this is a model for agents. We have seen ourselves how much compute, and how many tokens it can take to generate good binders using frontier structure-based models. Sometimes you need to generate tens of thousands of designs just to get a handful worth taking forward.
Now put this inside an AutoResearch loop. The agent has to continuously parse structures, inspect PDB/CIF files, compare candidates, run evaluations, modify the design, and repeat the whole thing again. It becomes extremely expensive very quickly.
Sequence space gives us a very different interface. LLMs are much more efficient at inspecting and manipulating compact molecular representations like SMILES than repeatedly operating over full structural files.
So LiteMol-1 becomes something like an infinite molecular canvas for the agent. For a given target and objective, the model can continuously propose what a biomolecule could look like. The agent can inspect those generations, take inspiration from them, preserve certain regions, edit others, optimize them, score them, and generate again.
Generate → inspect → evaluate → edit → generate again.
There is another problem I care a lot about. Most molecule design models today are heavily optimized around binding. But binding is only one part of whether something eventually becomes a therapeutic. What about ADME? Toxicity? Selectivity? Solubility? Membrane permeability? Synthesizability?
For this, we also built a Monte Carlo Tree Search-based multi-objective generation framework around LiteMol-1. Instead of combining everything into one score, the search keeps multiple strong candidates, each balancing the desired properties in a different way.
As our scoring functions and verifiers get better, the generation system gets better too. We can start steering molecules not just toward “binds well”, but toward a broader therapeutic design specification.
The bottleneck slowly moves from simply generating molecules to having sufficiently good verifiers and scoring functions to tell us what is actually worth generating. Check out our technical research blog post for all the details.
At LiteFold, our research is focused on engineering biomolecules and building systems that can carefully forecast their pre-clinical success.
To stay updated on our research, follow LiteFold.
Cheers!
LiteFold retweeted
reading 👀
Today, we are incredibly excited to present LiteMol-1, our very first foundation model from LiteFold.
Structure-based models like BoltzGen, O-Design, and RFdiffusion have become the de facto standard for designing biomolecules. However, they are expensive to run at scale. In many campaigns, we have to generate tens of thousands of designs and rigorously filter them down to a handful of top candidates.
More importantly, most molecule design systems are primarily optimized around binding. But what about everything else that makes a molecule a useful therapeutic: ADME, toxicity, drug-likeness, membrane permeability, synthesizability, selectivity, and more?
That’s where we introduce LiteMol-1, our first Multi-Molecule Foundation Diffusion Language Model, pre-trained from scratch. With a single set of weights, LiteMol-1 can conditionally generate small molecules, peptides, cyclic peptides, depsipeptides, peptides with ncAAs, macrocycles, and PROTACs.
You can generate molecules unconditionally or condition generation on a protein target sequence. You can in-paint molecules, preserve parts of an existing scaffold, generate non-canonical peptides, cyclize designs, and continuously edit and regenerate them.
We also introduce a Monte Carlo Tree Search framework for multi-objective molecular design. Instead of trying to make one molecule perfect at everything, the search keeps a set of promising molecules, each with different trade-offs across properties. This matters because molecular design is fundamentally not a single-objective optimization problem.
Finally, and probably the part we are most excited about: this is a model for Agents. LLMs are not particularly efficient interfaces for repeatedly reasoning over thousands of large PDB/CIF files inside an AutoResearch loop. Sequence space is different. SMILES and molecular sequences are compact, editable, and much easier for an agent to inspect, compare, modify, and reason over.
So we treat LiteMol-1 as an infinite molecular canvas.
The model generates possibilities. The agent takes inspiration from them, evaluates them, edits them, optimizes them, and generates again. The AutoResearch loop continues until it finds candidates that satisfy the given design objectives; while bringing in expensive structure prediction, docking, or simulation only when they are actually needed.
Our evaluations across peptide and small-molecule generation show that LiteMol-1 is competitive with, and in several settings on-par with or better than, frontier structure-based and sequence-based models, while operating at a fraction of the generation cost and time.
And this is only the first step. Check out our technical research blog post in the comments to learn more about LiteMol-1.