Levitate Bio
@levitate.bio
We're a small software company owned by the Rosetta Commons and dedicated to making easy to use and deploy cloud based protein engineering and molecular modeling software https://levitate.bio/subscribe
Pinned
Levitate Bio
@levitate.bio
· Nov 21
Levitate Bio
Elevate your Protein Design
levitate.bio
Hello! We're a software company which spun out of Cyrus Bio. We sell cloud based tools to help make state of the art protein engineering and modeling methods more accessible. We're owned by the Rosetta Commons Foundation which will use our profits to support academic research.
levitate.bio
levitate.bio
we've seen customers reaching back to physics based methods in order to solve their molecular modeling problems. In our latest post we explore how you can use the Rosetta "pocket opener" method with Boltz-2 to generate better protein-ligand models than Boltz-2 alone levitate.bio/boltz/ai/ml/...
Advancing Drug Discovery with Rosetta Pocket Protocols and Boltz-2: Finding and Modeling Druggable Binding Sites
In the evolving field of computational drug design, two of the most important challenges are identifying druggable surface pockets on proteins and predicting how strongly small molecules will bind to ...
levitate.bio
July 1, 2025 at 1:22 PM
we've seen customers reaching back to physics based methods in order to solve their molecular modeling problems. In our latest post we explore how you can use the Rosetta "pocket opener" method with Boltz-2 to generate better protein-ligand models than Boltz-2 alone levitate.bio/boltz/ai/ml/...
Reposted by Levitate Bio
How to train your model.
This immersive, hands-on, advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design. Join us for this Summer RosettaCon 2025 workshop/hackathon, more here: rosettacommons.org/2025/05/30/h...
This immersive, hands-on, advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design. Join us for this Summer RosettaCon 2025 workshop/hackathon, more here: rosettacommons.org/2025/05/30/h...
How to train your model
An advanced protein design Bootcamp / Hackathon software developer event Summer RosettaCon 2025 – Bootcamp / Hackathon – Application is open, apply here This immersive, hands-on event i…
rosettacommons.org
June 9, 2025 at 3:35 PM
How to train your model.
This immersive, hands-on, advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design. Join us for this Summer RosettaCon 2025 workshop/hackathon, more here: rosettacommons.org/2025/05/30/h...
This immersive, hands-on, advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design. Join us for this Summer RosettaCon 2025 workshop/hackathon, more here: rosettacommons.org/2025/05/30/h...
As @rolanddunbrack.bsky.social recently discovered, one of the issues with the ipTM score used AF2 to represent the ipTM score is that it is biased by disordered regions of the protein outside the binding interface. To address this, he implemented a new metric, ipSAE.
levitate.bio/alphafold/mu...
levitate.bio/alphafold/mu...
Fixing the Flaws in AlphaFold’s Interface Scoring: Meet Dunbrack’s ipSAE
Predicting protein-protein interactions Since AlphaFold2 was published, one of the major applications of the model was accurately predicting the structure of protein-protein interactions. By taking as...
levitate.bio
June 3, 2025 at 2:10 PM
As @rolanddunbrack.bsky.social recently discovered, one of the issues with the ipTM score used AF2 to represent the ipTM score is that it is biased by disordered regions of the protein outside the binding interface. To address this, he implemented a new metric, ipSAE.
levitate.bio/alphafold/mu...
levitate.bio/alphafold/mu...
there are still some real downsides to not actually modeling the physics
Its 2025 and two atoms STILL can exist in the same space according to AF3
June 3, 2025 at 2:05 PM
there are still some real downsides to not actually modeling the physics
Reposted by Levitate Bio
De novo #ai protein binder design with levitate.bio! Watch this video to see how it is done, with no code, no scripts, all in an easy to use GUI in the browser. youtu.be/87U_g8awaEE?...
Levitate Bio
Elevate your Protein Design
levitate.bio
March 17, 2025 at 11:39 PM
De novo #ai protein binder design with levitate.bio! Watch this video to see how it is done, with no code, no scripts, all in an easy to use GUI in the browser. youtu.be/87U_g8awaEE?...
BindCraft is a new AI de novo binder design tool from the Correia lab with 10-100% success rates. It's available today as an easy to use API using our API framework so you can deploy it in your own pipeline today.
Contact us at levitate.bio/contact to get started
www.biorxiv.org/content/10.1...
Contact us at levitate.bio/contact to get started
www.biorxiv.org/content/10.1...
BindCraft: one-shot design of functional protein binders
Protein–protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present B...
www.biorxiv.org
February 18, 2025 at 8:03 PM
BindCraft is a new AI de novo binder design tool from the Correia lab with 10-100% success rates. It's available today as an easy to use API using our API framework so you can deploy it in your own pipeline today.
Contact us at levitate.bio/contact to get started
www.biorxiv.org/content/10.1...
Contact us at levitate.bio/contact to get started
www.biorxiv.org/content/10.1...
RFDiffusion is great for de novo design but it can be a bit frustrating to use. Check our our new GUI for making de novo binder design fast and easy! www.youtube.com/watch?v=rwpL...
Using Levitate Bench for RFDiffusion based de novo Binder Design
YouTube video by Levitate Bio
www.youtube.com
January 29, 2025 at 5:17 PM
RFDiffusion is great for de novo design but it can be a bit frustrating to use. Check our our new GUI for making de novo binder design fast and easy! www.youtube.com/watch?v=rwpL...
Come work with us! We're hiring a Scientific Sales Specialist. This is the perfect job if you've got a BS in biology or biochemistry and are looking to start a career in software sales. No sales experience is necessary. For more details on the job and how to apply go to levitate.bio/careers
Levitate Bio
Elevate your Protein Design
levitate.bio
December 9, 2024 at 9:34 PM
Come work with us! We're hiring a Scientific Sales Specialist. This is the perfect job if you've got a BS in biology or biochemistry and are looking to start a career in software sales. No sales experience is necessary. For more details on the job and how to apply go to levitate.bio/careers
Reposted by Levitate Bio
I sometimes forget how flexible proteins are. It becomes really apparent when you use NMR states for an animation. That poor cofactor is getting pushed around a lot 😅
#sciart #blender3d #biocatalysis
#sciart #blender3d #biocatalysis
November 25, 2024 at 5:14 PM
I sometimes forget how flexible proteins are. It becomes really apparent when you use NMR states for an animation. That poor cofactor is getting pushed around a lot 😅
#sciart #blender3d #biocatalysis
#sciart #blender3d #biocatalysis
Reposted by Levitate Bio
Quiz: Side chains R K E Q I M have 9 chi1+chi2 rotamers. They are:
{g+g+} {g+t} {g+g-} {tg+} {tt} {tg-} {g-g+} {g-t} {g-g-}.
4 of these have high energy & v. low populations compared to rest. Which 4? Why?
Leu has only 2 good rotamers. Which ones? why?
Good struct bio final exam Question.
{g+g+} {g+t} {g+g-} {tg+} {tt} {tg-} {g-g+} {g-t} {g-g-}.
4 of these have high energy & v. low populations compared to rest. Which 4? Why?
Leu has only 2 good rotamers. Which ones? why?
Good struct bio final exam Question.
First reason is conceptual - rotamer libraries provide discrete conformations for sampling, which MM force fields do not (explicitly anyway). BBdep rotamer library ranks & scores (via -log(p)) rotamers as f(phi,psi). Rosetta/SCWRL take top 95% of probability density. Limits sampling to top rotamers.
November 24, 2024 at 10:37 PM
Quiz: Side chains R K E Q I M have 9 chi1+chi2 rotamers. They are:
{g+g+} {g+t} {g+g-} {tg+} {tt} {tg-} {g-g+} {g-t} {g-g-}.
4 of these have high energy & v. low populations compared to rest. Which 4? Why?
Leu has only 2 good rotamers. Which ones? why?
Good struct bio final exam Question.
{g+g+} {g+t} {g+g-} {tg+} {tt} {tg-} {g-g+} {g-t} {g-g-}.
4 of these have high energy & v. low populations compared to rest. Which 4? Why?
Leu has only 2 good rotamers. Which ones? why?
Good struct bio final exam Question.
Reposted by Levitate Bio
Beyond excited to introduce AlphaQubit, now published in
Nature!
AlphaQubit is a neural network for quantum error correction and achieves state-of-the-art accuracy on simulated and real-world data.
Nature!
AlphaQubit is a neural network for quantum error correction and achieves state-of-the-art accuracy on simulated and real-world data.
Learning high-accuracy error decoding for quantum processors - Nature
A recurrent, transformer-based neural network, called AlphaQubit, learns high-accuracy error decoding to suppress the errors that occur in quantum systems, opening the prospect of using neural-network...
nature.com
November 20, 2024 at 4:33 PM
Beyond excited to introduce AlphaQubit, now published in
Nature!
AlphaQubit is a neural network for quantum error correction and achieves state-of-the-art accuracy on simulated and real-world data.
Nature!
AlphaQubit is a neural network for quantum error correction and achieves state-of-the-art accuracy on simulated and real-world data.
Here's an interesting new paper from IPD: www.biorxiv.org/content/10.1...
Cyclic peptides are a compelling format for a drug but a lot of computational design tools don't handle them well. Here they modified AF2 and RFDiffusion with a rotational encoding 1/
Cyclic peptides are a compelling format for a drug but a lot of computational design tools don't handle them well. Here they modified AF2 and RFDiffusion with a rotational encoding 1/
Accurate de novo design of high-affinity protein binding macrocycles using deep learning
The development of macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource-intensive and provide little control over binding mode. Despite consi...
www.biorxiv.org
November 21, 2024 at 8:26 PM
Here's an interesting new paper from IPD: www.biorxiv.org/content/10.1...
Cyclic peptides are a compelling format for a drug but a lot of computational design tools don't handle them well. Here they modified AF2 and RFDiffusion with a rotational encoding 1/
Cyclic peptides are a compelling format for a drug but a lot of computational design tools don't handle them well. Here they modified AF2 and RFDiffusion with a rotational encoding 1/
Hello! We're a software company which spun out of Cyrus Bio. We sell cloud based tools to help make state of the art protein engineering and modeling methods more accessible. We're owned by the Rosetta Commons Foundation which will use our profits to support academic research.
levitate.bio
levitate.bio
Levitate Bio
Elevate your Protein Design
levitate.bio
November 21, 2024 at 5:39 PM
Hello! We're a software company which spun out of Cyrus Bio. We sell cloud based tools to help make state of the art protein engineering and modeling methods more accessible. We're owned by the Rosetta Commons Foundation which will use our profits to support academic research.
levitate.bio
levitate.bio