Alexander Ille
@alexander-ille.bsky.social
Postdoctoral Researcher @ Rutgers University
Passionate about molecular biology and AI/ML
Passionate about molecular biology and AI/ML
Pinned
Excited to share our work on modeling the human protein interactome in 3D. This currently includes 1,394 interaction structures predicted with Boltz-2. Grateful for the open-access resources making this possible!
Preprint: doi.org/10.1101/2025...
Preprint: doi.org/10.1101/2025...
State of the art!
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 9:19 PM
State of the art!
Excited to share an update of our work on modeling the human protein interactome in 3D using Boltz-2. Large-scale protein complex prediction allows for exploring structurally-informed biological networks.
Preprint on bioRxiv: doi.org/10.1101/2025...
Preprint on bioRxiv: doi.org/10.1101/2025...
August 21, 2025 at 4:22 PM
Excited to share an update of our work on modeling the human protein interactome in 3D using Boltz-2. Large-scale protein complex prediction allows for exploring structurally-informed biological networks.
Preprint on bioRxiv: doi.org/10.1101/2025...
Preprint on bioRxiv: doi.org/10.1101/2025...
Reposted by Alexander Ille
Eat your carrots or you'll go blind! The biochemical reason for this warning is that we need retinal, vitamin A, to form the pigment that absorbs light in our eyes.
More at Molecule of the Month: pdb101.rcsb.org/motm/66
#PeakPerformance
More at Molecule of the Month: pdb101.rcsb.org/motm/66
#PeakPerformance
August 20, 2025 at 4:22 PM
Eat your carrots or you'll go blind! The biochemical reason for this warning is that we need retinal, vitamin A, to form the pigment that absorbs light in our eyes.
More at Molecule of the Month: pdb101.rcsb.org/motm/66
#PeakPerformance
More at Molecule of the Month: pdb101.rcsb.org/motm/66
#PeakPerformance
Excited to share our work on modeling the human protein interactome in 3D. This currently includes 1,394 interaction structures predicted with Boltz-2. Grateful for the open-access resources making this possible!
Preprint: doi.org/10.1101/2025...
Preprint: doi.org/10.1101/2025...
July 4, 2025 at 11:38 AM
Excited to share our work on modeling the human protein interactome in 3D. This currently includes 1,394 interaction structures predicted with Boltz-2. Grateful for the open-access resources making this possible!
Preprint: doi.org/10.1101/2025...
Preprint: doi.org/10.1101/2025...
Excited to share a new article I co-authored on the relationship between biological sequence and structure! We look back to historic hypotheses, and look forward to how AI/ML models may be developed to predict protein conformational dynamics. Paper: doi.org/10.1063/4.00...
June 24, 2025 at 9:10 PM
Excited to share a new article I co-authored on the relationship between biological sequence and structure! We look back to historic hypotheses, and look forward to how AI/ML models may be developed to predict protein conformational dynamics. Paper: doi.org/10.1063/4.00...
Hemoglobin, the biomolecule that breathes, modeled with Boltz-2.
With the recent release of #Boltz2, I gave it a try for modeling hemoglobin. Hemoglobin structures were likely included for training, and this was just a fun test, but it’s awesome to see this modeling in action!
With the recent release of #Boltz2, I gave it a try for modeling hemoglobin. Hemoglobin structures were likely included for training, and this was just a fun test, but it’s awesome to see this modeling in action!
June 18, 2025 at 9:08 PM
Hemoglobin, the biomolecule that breathes, modeled with Boltz-2.
With the recent release of #Boltz2, I gave it a try for modeling hemoglobin. Hemoglobin structures were likely included for training, and this was just a fun test, but it’s awesome to see this modeling in action!
With the recent release of #Boltz2, I gave it a try for modeling hemoglobin. Hemoglobin structures were likely included for training, and this was just a fun test, but it’s awesome to see this modeling in action!
Truly remarkable work. Looking forward to using it!
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀
June 8, 2025 at 7:34 PM
Truly remarkable work. Looking forward to using it!
Dynamic insight into DNA → RNA → protein. Great work!
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
May 16, 2025 at 3:39 PM
Dynamic insight into DNA → RNA → protein. Great work!
Reposted by Alexander Ille
New RCSB PDB publication--
Read how Mol* can be used to visualize and analyze the influenza A H5N1 virus proteome
pdb101.rcsb.org/news...
Read how Mol* can be used to visualize and analyze the influenza A H5N1 virus proteome
pdb101.rcsb.org/news...
PDB101: Paper Published: Visualizing and analyzing 3D biomolecular structures using Mol*
PDB-101: Training, Outreach, and Education portal of RCSB PDB
pdb101.rcsb.org
April 17, 2025 at 4:33 PM
New RCSB PDB publication--
Read how Mol* can be used to visualize and analyze the influenza A H5N1 virus proteome
pdb101.rcsb.org/news...
Read how Mol* can be used to visualize and analyze the influenza A H5N1 virus proteome
pdb101.rcsb.org/news...
Computational capacity of life in relation to the universe | Science Advances www.science.org/doi/10.1126/...
Computational capacity of life in relation to the universe
The discovery of life processing with UV-excited qubits supports a conjecture relative to the computing capacity of the universe.
www.science.org
April 4, 2025 at 3:10 PM
Computational capacity of life in relation to the universe | Science Advances www.science.org/doi/10.1126/...
Creative use of AlphaFold for predicting oligomeric states of proteins, nice work.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AlphaFold can be used to predict the oligomeric states of proteins
Homooligomerisation is a prevalent and important process that many proteins undergo to form the quaternary structure required to carry out their biological functions. However, determining the oligomer...
www.biorxiv.org
April 2, 2025 at 4:08 PM
Creative use of AlphaFold for predicting oligomeric states of proteins, nice work.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Predictomes (Schmid & Walter, 2025). This looks very useful!
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid and Walter train a classifier that discerns functionally relevant structure
predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer,
and they use this co...
www.cell.com
March 24, 2025 at 4:50 PM
Predictomes (Schmid & Walter, 2025). This looks very useful!
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...