Ariane Nunes Alves
@anunesalves.bsky.social
Computational biochemist (ligand binding kinetics, crowding)
Junior group leader at the Technical University Berlin
Associate editor at the Journal of Chemical Information and Modeling
Brazilian in Germany
Junior group leader at the Technical University Berlin
Associate editor at the Journal of Chemical Information and Modeling
Brazilian in Germany
Happy to share the manuscript from @apoorvam.bsky.social, Mariona, Max, Chiara and me, where we used molecular dynamics simulations to investigate the effects of molecular glues over protein-protein complexes involving FKBP.
arxiv.org/abs/2510.26806
#compchem
arxiv.org/abs/2510.26806
#compchem
November 5, 2025 at 8:00 AM
Happy to share the manuscript from @apoorvam.bsky.social, Mariona, Max, Chiara and me, where we used molecular dynamics simulations to investigate the effects of molecular glues over protein-protein complexes involving FKBP.
arxiv.org/abs/2510.26806
#compchem
arxiv.org/abs/2510.26806
#compchem
Great book! Explains a lot about the toxic positivity that I see in other social medias.
August 25, 2025 at 8:50 PM
Great book! Explains a lot about the toxic positivity that I see in other social medias.
Tour with my research group yesterday at the Natural History Museum in Berlin! With T. rex skull in the back!
@farzinsohraby.bsky.social
@farzinsohraby.bsky.social
August 8, 2025 at 9:51 AM
Tour with my research group yesterday at the Natural History Museum in Berlin! With T. rex skull in the back!
@farzinsohraby.bsky.social
@farzinsohraby.bsky.social
We characterized for the first time paths for agonist and antagonist dissociation from the Toll-like receptor 8.
Two paths were found.
Interestingly, some ligands have clear path preferences: the agonist uses only the external path, and the cationic antagonists use only the internal path. (2/3)
Two paths were found.
Interestingly, some ligands have clear path preferences: the agonist uses only the external path, and the cationic antagonists use only the internal path. (2/3)
July 10, 2025 at 7:21 AM
We characterized for the first time paths for agonist and antagonist dissociation from the Toll-like receptor 8.
Two paths were found.
Interestingly, some ligands have clear path preferences: the agonist uses only the external path, and the cationic antagonists use only the internal path. (2/3)
Two paths were found.
Interestingly, some ligands have clear path preferences: the agonist uses only the external path, and the cationic antagonists use only the internal path. (2/3)
Happy to share that the work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists was accepted at JCIM! (1/3)
#compchem
pubs.acs.org/doi/10.1021/...
#compchem
pubs.acs.org/doi/10.1021/...
July 10, 2025 at 7:21 AM
Happy to share that the work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists was accepted at JCIM! (1/3)
#compchem
pubs.acs.org/doi/10.1021/...
#compchem
pubs.acs.org/doi/10.1021/...
PhD defense at the Humboldt University today.
July 2, 2025 at 1:19 PM
PhD defense at the Humboldt University today.
My PhD student @apoorvam.bsky.social will be in the EBSA meeting in Rome next week to represent our lab.
Go check her poster about the multi-scale method she is developing to simulate the bacterial cytoplasm.
Go check her poster about the multi-scale method she is developing to simulate the bacterial cytoplasm.
June 25, 2025 at 8:16 AM
My PhD student @apoorvam.bsky.social will be in the EBSA meeting in Rome next week to represent our lab.
Go check her poster about the multi-scale method she is developing to simulate the bacterial cytoplasm.
Go check her poster about the multi-scale method she is developing to simulate the bacterial cytoplasm.
My PhD student Daniil Lepikhov delivered a great talk last Friday about his results in benchmarking diffusion models for protein-ligand complex structure prediction at the annual retreat of his graduate school, BIG-NSE.
#compchem
#compchem
June 15, 2025 at 2:37 PM
My PhD student Daniil Lepikhov delivered a great talk last Friday about his results in benchmarking diffusion models for protein-ligand complex structure prediction at the annual retreat of his graduate school, BIG-NSE.
#compchem
#compchem
We also observe that the main bottleneck for ligand binding can shift between two states with different bottleneck widths, a feature which can be exploited to modulate the access of small molecules to the catalytic site of [NiFe] hydrogenases. (3/3)
June 3, 2025 at 7:18 AM
We also observe that the main bottleneck for ligand binding can shift between two states with different bottleneck widths, a feature which can be exploited to modulate the access of small molecules to the catalytic site of [NiFe] hydrogenases. (3/3)
We observe path symmetry for binding and unbinding, and we propose the used of the pathway probabilities presented as a benchmark for enhanced sampling methods which investigate protein-ligand binding. (2/3)
June 3, 2025 at 7:18 AM
We observe path symmetry for binding and unbinding, and we propose the used of the pathway probabilities presented as a benchmark for enhanced sampling methods which investigate protein-ligand binding. (2/3)
Lunch with my group today to say goodbye to Laura (off to a PhD in Belgium) and to welcome Chiara and Philipp!
May 23, 2025 at 1:12 PM
Lunch with my group today to say goodbye to Laura (off to a PhD in Belgium) and to welcome Chiara and Philipp!
I had the pleasure to give a talk at Unicamp yesterday!
lovely to discuss science in Portuguese in my home country.
🥰
lovely to discuss science in Portuguese in my home country.
🥰
April 4, 2025 at 4:55 PM
I had the pleasure to give a talk at Unicamp yesterday!
lovely to discuss science in Portuguese in my home country.
🥰
lovely to discuss science in Portuguese in my home country.
🥰
In the last weeks I had the pleasure to attend a lot of fun events! Thanks to @adrianroitberg.bsky.social and @perezlab.bsky.social for the invitation to talk at the Sanibel Symposium, and thanks to @athinaganathan.bsky.social for the invitation to talk at the Indian Biophysical Society meeting!
March 15, 2025 at 12:46 PM
In the last weeks I had the pleasure to attend a lot of fun events! Thanks to @adrianroitberg.bsky.social and @perezlab.bsky.social for the invitation to talk at the Sanibel Symposium, and thanks to @athinaganathan.bsky.social for the invitation to talk at the Indian Biophysical Society meeting!
- best posters:
Piotr Chyzy
Farzin Sohraby
Miriam Jäger
@parsec93.bsky.social
Thanks a lot to everyone who attended! I had a great time!
I hope to see all of you soon to discuss more ligand binding kinetics!
Piotr Chyzy
Farzin Sohraby
Miriam Jäger
@parsec93.bsky.social
Thanks a lot to everyone who attended! I had a great time!
I hope to see all of you soon to discuss more ligand binding kinetics!
March 15, 2025 at 11:27 AM
- best posters:
Piotr Chyzy
Farzin Sohraby
Miriam Jäger
@parsec93.bsky.social
Thanks a lot to everyone who attended! I had a great time!
I hope to see all of you soon to discuss more ligand binding kinetics!
Piotr Chyzy
Farzin Sohraby
Miriam Jäger
@parsec93.bsky.social
Thanks a lot to everyone who attended! I had a great time!
I hope to see all of you soon to discuss more ligand binding kinetics!
Thanks to our sponsors, Wiley, Journal of Molecular Recognition, ChemPhysChem, @chemistryeurope.bsky.social, @schrodingerinc.bsky.social and Kvantify, we were able to award prizes to young investigators:
- best oral contribution:
Sina Safaei
- best oral contribution:
Sina Safaei
March 15, 2025 at 11:27 AM
Thanks to our sponsors, Wiley, Journal of Molecular Recognition, ChemPhysChem, @chemistryeurope.bsky.social, @schrodingerinc.bsky.social and Kvantify, we were able to award prizes to young investigators:
- best oral contribution:
Sina Safaei
- best oral contribution:
Sina Safaei
The CECAM workshop "Predicting and understanding drug-target binding kinetics via molecular simulations", organized by @herrflow.bsky.social, @rebecca-wade.bsky.social, Giovanni Bottegoni and me, ended last Wednesday.
March 15, 2025 at 11:27 AM
The CECAM workshop "Predicting and understanding drug-target binding kinetics via molecular simulations", organized by @herrflow.bsky.social, @rebecca-wade.bsky.social, Giovanni Bottegoni and me, ended last Wednesday.
Group picture of the @cecamevents.bsky.social workshop on ligand binding kinetics!
#compchem
@herrflow.bsky.social @rebecca-wade.bsky.social
#compchem
@herrflow.bsky.social @rebecca-wade.bsky.social
March 11, 2025 at 8:16 AM
Group picture of the @cecamevents.bsky.social workshop on ligand binding kinetics!
#compchem
@herrflow.bsky.social @rebecca-wade.bsky.social
#compchem
@herrflow.bsky.social @rebecca-wade.bsky.social
March 10, 2025 at 1:13 PM
#compchem
New work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists. Interestingly, some ligands showed clear path preference:...
chemrxiv.org/engage/chemr...
New work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists. Interestingly, some ligands showed clear path preference:...
chemrxiv.org/engage/chemr...
March 7, 2025 at 1:37 PM
#compchem
New work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists. Interestingly, some ligands showed clear path preference:...
chemrxiv.org/engage/chemr...
New work by Valerij Talagayev, Gerhard Wolber and me using tauRAMD to characterize unbinding paths of TLR8 agonist and antagonists. Interestingly, some ligands showed clear path preference:...
chemrxiv.org/engage/chemr...
The Indian Biophysical Society meeting started!
Come to my plenary lecture later today to hear about #compchem, MD simulations, machine learning and hydrogenases.
Come to my plenary lecture later today to hear about #compchem, MD simulations, machine learning and hydrogenases.
March 6, 2025 at 5:05 AM
The Indian Biophysical Society meeting started!
Come to my plenary lecture later today to hear about #compchem, MD simulations, machine learning and hydrogenases.
Come to my plenary lecture later today to hear about #compchem, MD simulations, machine learning and hydrogenases.
The deers at IIT Madras and I are looking forward to the start of the Indian Biophysical Society meeting tomorrow!
🤩
🤩
March 5, 2025 at 1:16 PM
The deers at IIT Madras and I are looking forward to the start of the Indian Biophysical Society meeting tomorrow!
🤩
🤩