Vojtech Spiwok
@spiwokv.bsky.social
📤 860
📥 1984
📝 163
Molecular modeling, simulations, metadynamics, machine learning
pinned post!
Our new ML conformational samppler out in
#jctc
#acs
pubs.acs.org/doi/10.1021/...
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Generative Autoencoders Coupled to Monte Carlo Simulation Allow Efficient Protein Conformation Sampling
Molecular simulations of proteins are well-known to be computationally expensive. Here, we present a new latent-space-based method for modeling protein conformational flexibility at a very affordable computational cost. The method is data-driven and employs an autoencoder-based machine learning model for reversible dimensionality reduction of diverse conformations of the protein studied. Next, samples are selected from the low-dimensional latent space via Monte Carlo sampling. The folding and unfolding of the miniproteins can be sampled in minutes of computational time. We validated the method on four model systems: Tryptophan Cage, nonfolding variant of Tryptophan Cage, Villin headpiece, and human β-2-syntrophin PDZ domain (miniproteins with 20, 20, 35, and 95 residues, respectively). All systems were modeled at an all-atom resolution. Tryptophan Cage and Villin miniproteins show very similar populations of folded/unfolded states sampled by Monte Carlo simulations as the reference MD trajectories calculated by D. E. Shaw Research.
https://pubs.acs.org/doi/10.1021/acs.jctc.5c01813
14 days ago
1
9
3
Our new ML conformational samppler out in
#jctc
#acs
pubs.acs.org/doi/10.1021/...
loading . . .
Generative Autoencoders Coupled to Monte Carlo Simulation Allow Efficient Protein Conformation Sampling
Molecular simulations of proteins are well-known to be computationally expensive. Here, we present a new latent-space-based method for modeling protein conformational flexibility at a very affordable computational cost. The method is data-driven and employs an autoencoder-based machine learning model for reversible dimensionality reduction of diverse conformations of the protein studied. Next, samples are selected from the low-dimensional latent space via Monte Carlo sampling. The folding and unfolding of the miniproteins can be sampled in minutes of computational time. We validated the method on four model systems: Tryptophan Cage, nonfolding variant of Tryptophan Cage, Villin headpiece, and human β-2-syntrophin PDZ domain (miniproteins with 20, 20, 35, and 95 residues, respectively). All systems were modeled at an all-atom resolution. Tryptophan Cage and Villin miniproteins show very similar populations of folded/unfolded states sampled by Monte Carlo simulations as the reference MD trajectories calculated by D. E. Shaw Research.
https://pubs.acs.org/doi/10.1021/acs.jctc.5c01813
14 days ago
1
9
3
Andrea Guljas on AI and protein dynamics
#ml4ngpWarsaw
19 days ago
0
3
0
Lukáš Žídek on mycobacterial IDPs
#ml4ngpWarsaw
21 days ago
0
3
0
Dirk Linke on
#IDP
in prokaryotes
#ml4ngpWarsaw
21 days ago
0
2
0
Zsuzsa Dosztanyi on
#IDP
variant predictors
#ml4ngpWarsaw
21 days ago
0
3
0
Michael Feig doing microphone check before his talk on peptides in condensates
#ml4ngpWarsaw
21 days ago
0
3
0
Michael Heinzinger on protein
#llm
and dynamics
#ml4ngpWarsaw
21 days ago
0
5
0
Rohit Pappu
@rohitpappu68.bsky.social
keynote talk
#ml4ngpWarsaw
21 days ago
0
2
1
Kick off of the ML4NGP meeting in Warsaw by Alexander Monzon
#IDP
#ml4ngpWarsaw
21 days ago
0
4
0
Sebastian Hiller on integrative NMR
#pps2026
about 1 month ago
0
4
2
reposted by
Vojtech Spiwok
Simon Fisher
about 1 month ago
Been training for this moment my whole life.
21
480
102
Andrea Soranno on IDP biophysics
#ppps2026
about 1 month ago
0
4
1
Tomas Pluskal
@pluskal-lab.org
on plants, their products and AI
#pps2026
about 1 month ago
0
11
3
Agnes Toth-Petroczy
@tothpetroczylab.bsky.social
on IDPs
#pps2026
about 1 month ago
0
3
2
Basile Wicky
@ethz.ch
on protein design
#pps2026
about 1 month ago
0
4
1
Ahrum Son on protein structural changes in alzheimer’s disease
#pps2026
about 1 month ago
0
2
1
Lukasz Joachimiak on amyloids
#pps2026
about 1 month ago
0
2
0
Gennady Verkhivker on AI and allostery in protein kinases
#pps2026
about 1 month ago
0
5
1
Sameer Velankar
@pdbeurope.bsky.social
@ebi.embl.org
ready to his talk on AI in biology
#pps2026
about 1 month ago
0
3
1
Alena Khmelinskaia
@akhmelinlab.bsky.social
promoting
@rosettacommons.bsky.social
-Con after her amazing talk on design of protein nanostructures
#pps2026
about 1 month ago
0
4
2
George Makhatadze changes title of his talk
#pps20026
about 1 month ago
0
1
0
On neurodegeneration by Nikolay Dokholyan
#pps2026
about 1 month ago
0
2
1
Stephen Fried on folding by mass spec
#pps2026
about 1 month ago
0
2
0
Patricia Clark on silent mutations and protein folding
#pps2026
about 1 month ago
0
3
1
Eugene Shakhnovich on chaperonines helping bacteia to resist antibiotics
#pps2026
about 1 month ago
1
4
1
Next speaker is Michele Vendruscolo on dugging undruggable
#pps2026
about 1 month ago
0
4
1
And great opening of Prague Protein Spring by David Baker
@nd-bakerlab.bsky.social
#pps2026
about 1 month ago
2
3
2
Opening of Prague Protein Spring 2026 by Jan Konvalinka
#pps2026
about 1 month ago
0
5
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Prague Protein Spring 2026
#pps2026
ready to start
about 1 month ago
0
4
0
Analysis and Sampling of Molecular Simulations with Adversarial Autoencoders by
@guted.bsky.social
doi.org/10.1063/5.03...
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Analysis and sampling of molecular simulations with adversarial autoencoders
The design of good collective variables for analysis and the enhancement of sampling of molecular simulations is not a trivial task. It often relies on the know
https://doi.org/10.1063/5.0320541
2 months ago
0
9
3
reposted by
Vojtech Spiwok
3 months ago
Best student question to be awarded
#novehrady2026
0
3
1
reposted by
Vojtech Spiwok
3 months ago
The winner of the best student talk is Andrej Tekel from
@sciencecharles.bsky.social
@czp.cuni.cz
#novehrady2026
0
5
2
reposted by
Vojtech Spiwok
3 months ago
Winners of the best poster awards are Adéla Fejfarová, Jiří Srogoň and Róbert Šándor
#novehrady2026
0
5
3
Lenka Faltova
@ethz.ch
on biomolecular condensates
#llps
#novehrady2026
3 months ago
0
4
2
Pub qiuz 1st place Enfants terribles!
#novehrady2026
3 months ago
0
2
1
Pub qiuz 2rd place Zluta P!
#novehrady2026
3 months ago
0
2
1
Pub qiuz 3rd place Anticrystals!
#novehrady2026
3 months ago
0
4
1
reposted by
Vojtech Spiwok
3 months ago
Pub quiz in
#novehrady2026
0
4
2
reposted by
Vojtech Spiwok
Klara Hlouchova lab
7 months ago
Can proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design.
tinyurl.com/37t8br4v
#ProteinDesign
#OriginsOfLife
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Ancient amino acid sets enable stable protein folds
Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...
https://tinyurl.com/37t8br4v
1
25
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reposted by
Vojtech Spiwok
8 months ago
22nd Structural Biology Club online on 26th November 2025, 1pm CE: Structures in solution: BioSAXS at BM29 ESRF by Petra Pernot & Cryo-EM data processing in CCP-EM Doppio by Colin M. Palmer
cssb.structbio.org/22nd-structu...
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8
4
Homology modeling
8 months ago
0
6
1
reposted by
Vojtech Spiwok
8 months ago
Protein Production Hands-On Workshop Dates: December 2 – 4, 2025 Venue: BIOCEV, Vestec Registration Deadline: October 31, 2025 Cost: Free of charge (accommodation not included) Registration Link:
forms.biocev.org/index.php/14...
Workshop Page:
www.ibt.cas.cz/en/core-faci...
0
5
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Our first protein design paper out in Protein Science
onlinelibrary.wiley.com/doi/10.1002/...
9 months ago
3
15
4
Pranam Chatterjee
@pranam.bsky.social
and his first AI-generated baby
#CecamLLMLugano
9 months ago
0
2
0
Traveling to "Generative AI and large language models for protein modeling across sequence-structure-function scales : From predicting protein dynamics to programmable biology and drug design" in Lugano
#CecamAILugano
@cecamevents.bsky.social
9 months ago
2
10
0
Max Bonomi
@bonomimax.bsky.social
on IDP modeling by AI
@cecamevents.bsky.social
#CecamLLMLugano
9 months ago
0
5
1
Prof. Michele Vendruscolo Dr. Zsuzsanna Dosztányi ML4NGP Connect series, organized as part of the ongoing activities of the ELIXIR 3D-BioInfo Community and in collaboration with ISCB and 3DSIG. 📢 Date & Time: 30 September 2025 | 17:00-18:00 CEST Online
elixir-europe.org/events/unstr...
9 months ago
0
8
0
Happy birthday ČSBMB
#CSBMB2025
9 months ago
0
3
1
Hana Cahová (
@iocbprague.bsky.social
) awarded a medal by CSBMB
#CSBMB2025
9 months ago
0
4
1
Kickoff of XXVIII-th congress of the Czech Society for Biochemistry and Molecular Biology (
@febspress.bsky.social
member )
9 months ago
1
0
0
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