Michele Invernizzi
@invemichele.bsky.social
Computational physicist at https://peptone.io
PhD @GroupParrinello, PostDoc @franknoe.bsky.social
Disordered Proteins, AI for Science, Molecular Dynamics, Enhanced Sampling
🔗 https://scholar.google.com/citations?user=fnJktPAAAAAJ
PhD @GroupParrinello, PostDoc @franknoe.bsky.social
Disordered Proteins, AI for Science, Molecular Dynamics, Enhanced Sampling
🔗 https://scholar.google.com/citations?user=fnJktPAAAAAJ
Pinned
See you at #NeurIPS2024, where we are presenting the latest Peptone.io paper @workshopmlsb.bsky.social
www.mlsb.io/papers_2024/...
www.mlsb.io/papers_2024/...
Reposted by Michele Invernizzi
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
October 20, 2025 at 11:26 AM
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
We have a job opening at Peptone.io for an ML researcher.
Come help us find new ways to understand and drug intrinsically disordered proteins (IDPs), it's a very interesting and important problem!
Link in the reply ↓
Come help us find new ways to understand and drug intrinsically disordered proteins (IDPs), it's a very interesting and important problem!
Link in the reply ↓
May 9, 2025 at 3:26 PM
We have a job opening at Peptone.io for an ML researcher.
Come help us find new ways to understand and drug intrinsically disordered proteins (IDPs), it's a very interesting and important problem!
Link in the reply ↓
Come help us find new ways to understand and drug intrinsically disordered proteins (IDPs), it's a very interesting and important problem!
Link in the reply ↓
Reposted by Michele Invernizzi
The plan at FutureHouse has been to build scientific agents for discoveries. We’ve spent the last year researching the best way to make agents. We’ve made a ton of progress and now we’ve engineered them to be used at scale, by anyone. Free and on API.
May 1, 2025 at 4:16 PM
The plan at FutureHouse has been to build scientific agents for discoveries. We’ve spent the last year researching the best way to make agents. We’ve made a ton of progress and now we’ve engineered them to be used at scale, by anyone. Free and on API.
Reposted by Michele Invernizzi
Presenting one of my favorite manuscripts I've ever worked on:
"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"
www.biorxiv.org/content/10.1...
by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social
"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"
www.biorxiv.org/content/10.1...
by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social
April 30, 2025 at 5:45 PM
Presenting one of my favorite manuscripts I've ever worked on:
"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"
www.biorxiv.org/content/10.1...
by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social
"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"
www.biorxiv.org/content/10.1...
by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social
Reposted by Michele Invernizzi
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
delalamo.xyz
April 27, 2025 at 2:16 PM
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
Reposted by Michele Invernizzi
Presenting our work on minimum energy path generation between two states for physical systems at the FPI Workshop at @ICLR tomorrow! Scaling up to solvated BPTI and observing the same conformational changes as long reference MD with six orders fewer force field evals! Drop by!
April 27, 2025 at 4:25 PM
Presenting our work on minimum energy path generation between two states for physical systems at the FPI Workshop at @ICLR tomorrow! Scaling up to solvated BPTI and observing the same conformational changes as long reference MD with six orders fewer force field evals! Drop by!
Reposted by Michele Invernizzi
New preprint on arXiv! We propose a new technique to compute kinetic rates using multiple independent non-equilibrium (ratchet&pawl MD) simulations!
We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!
We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!
Kinetic rates calculation via non-equilibrium dynamics
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrati...
arxiv.org
April 23, 2025 at 6:08 AM
New preprint on arXiv! We propose a new technique to compute kinetic rates using multiple independent non-equilibrium (ratchet&pawl MD) simulations!
We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!
We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!
Reposted by Michele Invernizzi
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 17, 2025 at 7:11 PM
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
Reposted by Michele Invernizzi
BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 7, 2025 at 7:01 AM
BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Michele Invernizzi
Wondering how to predict protein flexibility in a sec? No time to run MD simulations but want to go beyond pLDDT? Check out BBFlow
arxiv.org/html/2503.05...
Useful in particular for de novo designs.
Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social
arxiv.org/html/2503.05...
Useful in particular for de novo designs.
Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social
March 31, 2025 at 11:37 AM
Wondering how to predict protein flexibility in a sec? No time to run MD simulations but want to go beyond pLDDT? Check out BBFlow
arxiv.org/html/2503.05...
Useful in particular for de novo designs.
Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social
arxiv.org/html/2503.05...
Useful in particular for de novo designs.
Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social
Reposted by Michele Invernizzi
Small proteins can be more complex than they look!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
March 26, 2025 at 4:21 PM
Small proteins can be more complex than they look!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
Reposted by Michele Invernizzi
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
March 20, 2025 at 3:02 PM
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
Reposted by Michele Invernizzi
Straight to the reading list:
Training a machine learning model based on residues with missing NMR assignments as a proxy for protein motion
Training a machine learning model based on residues with missing NMR assignments as a proxy for protein motion
Learning millisecond protein dynamics from what is missing in NMR spectra https://www.biorxiv.org/content/10.1101/2025.03.19.642801v1
March 19, 2025 at 10:15 PM
Straight to the reading list:
Training a machine learning model based on residues with missing NMR assignments as a proxy for protein motion
Training a machine learning model based on residues with missing NMR assignments as a proxy for protein motion
Reposted by Michele Invernizzi
Very excited for my first BSKY post. We present a new method, Loxodynamics, for exploring chemical and catalytic reaction space!
Exploring Chemistry and Catalysis by Biasing Skewed Distributions via Deep Learning
Authors: Zhikun Zhang, GiovanniMaria Piccini
DOI: 10.26434/chemrxiv-2025-cvb1v
Authors: Zhikun Zhang, GiovanniMaria Piccini
DOI: 10.26434/chemrxiv-2025-cvb1v
March 13, 2025 at 9:19 AM
Very excited for my first BSKY post. We present a new method, Loxodynamics, for exploring chemical and catalytic reaction space!
Reposted by Michele Invernizzi
Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB
authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei
authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei
March 12, 2025 at 9:35 PM
Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB
authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei
authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei
Reposted by Michele Invernizzi
The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...
PLUMED Tutorials: A collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes
doi.org
March 4, 2025 at 2:13 PM
The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...
Reposted by Michele Invernizzi
As a peek toward where we're headed:
Right now, CADD scientists are forced to use the same model week after week, even if new experimental data says the model is inaccurate.
If we can fine- models, we can exploit that data to systematically improve our predictions week by week!
Right now, CADD scientists are forced to use the same model week after week, even if new experimental data says the model is inaccurate.
If we can fine- models, we can exploit that data to systematically improve our predictions week by week!
February 19, 2025 at 7:36 PM
As a peek toward where we're headed:
Right now, CADD scientists are forced to use the same model week after week, even if new experimental data says the model is inaccurate.
If we can fine- models, we can exploit that data to systematically improve our predictions week by week!
Right now, CADD scientists are forced to use the same model week after week, even if new experimental data says the model is inaccurate.
If we can fine- models, we can exploit that data to systematically improve our predictions week by week!
Reposted by Michele Invernizzi
The BioEmu-1 model and inference code are now public under MIT license!!!
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
February 19, 2025 at 8:17 PM
The BioEmu-1 model and inference code are now public under MIT license!!!
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Reposted by Michele Invernizzi
I am hiring a postdoctoral scholar with a start date summer or fall 2025. Projects will be focused on thermodynamically consistent generative models, broadly defined. If you’re interested, please send a CV and one paragraph about why you think you’d be a good fit to rotskoff@stanford.edu
December 23, 2024 at 5:31 PM
I am hiring a postdoctoral scholar with a start date summer or fall 2025. Projects will be focused on thermodynamically consistent generative models, broadly defined. If you’re interested, please send a CV and one paragraph about why you think you’d be a good fit to rotskoff@stanford.edu
Reposted by Michele Invernizzi
It’s been 20 years today since my first paper on intrinsically disordered proteins
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
doi.org/10.1021/ja04...
and I thought I would tell the somewhat random path that led to this paper. 1/n
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
doi.org/10.1021/ja04...
and I thought I would tell the somewhat random path that led to this paper. 1/n
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
The intrinsically disordered protein α-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of α-synuclein consists of a broad distribution of...
doi.org
December 21, 2024 at 5:09 PM
It’s been 20 years today since my first paper on intrinsically disordered proteins
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
doi.org/10.1021/ja04...
and I thought I would tell the somewhat random path that led to this paper. 1/n
Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
doi.org/10.1021/ja04...
and I thought I would tell the somewhat random path that led to this paper. 1/n
Reposted by Michele Invernizzi
With today's report outlining risks on mirror life www.science.org/doi/full/10.... many have asked:
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Confronting risks of mirror life
Broad discussion is needed to chart a path forward.
www.science.org
December 12, 2024 at 9:40 PM
With today's report outlining risks on mirror life www.science.org/doi/full/10.... many have asked:
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Reposted by Michele Invernizzi
In his book “The Nature of Statistical Learning” V. Vapnik wrote:
“When solving a given problem, try to avoid a more general problem as an intermediate step”
“When solving a given problem, try to avoid a more general problem as an intermediate step”
December 12, 2024 at 5:19 PM
In his book “The Nature of Statistical Learning” V. Vapnik wrote:
“When solving a given problem, try to avoid a more general problem as an intermediate step”
“When solving a given problem, try to avoid a more general problem as an intermediate step”
See you at #NeurIPS2024, where we are presenting the latest Peptone.io paper @workshopmlsb.bsky.social
www.mlsb.io/papers_2024/...
www.mlsb.io/papers_2024/...
December 11, 2024 at 6:53 PM
See you at #NeurIPS2024, where we are presenting the latest Peptone.io paper @workshopmlsb.bsky.social
www.mlsb.io/papers_2024/...
www.mlsb.io/papers_2024/...