Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
CASP RNA SIG
Welcome nucleic acid enthusiasts to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, buildi...
www.youtube.com
October 30, 2025 at 2:45 PM
Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...
September 24, 2025 at 4:21 PM
The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...
CASP16 group picture - in Punta Cana
December 20, 2024 at 3:17 PM
CASP16 group picture - in Punta Cana
We used @gromacs.bsky.social + @plumed.org and a custom replica exchange method developed by Olivier. More details in our presentation (www.predictioncenter.org/casp16/doc/p...) and abstract (www.predictioncenter.org/casp16/doc/C...). PLUMED tutorial at www.plumed-tutorials.org/lessons/24/0...
www.predictioncenter.org
December 18, 2024 at 9:50 AM
We used @gromacs.bsky.social + @plumed.org and a custom replica exchange method developed by Olivier. More details in our presentation (www.predictioncenter.org/casp16/doc/p...) and abstract (www.predictioncenter.org/casp16/doc/C...). PLUMED tutorial at www.plumed-tutorials.org/lessons/24/0...
However, CASP16 participants, including automated methods trRosettaRNA and AF3, are more accurate at predicting secondary structure than popular secondary structure prediction algorithms.
May 20, 2025 at 9:01 PM
However, CASP16 participants, including automated methods trRosettaRNA and AF3, are more accurate at predicting secondary structure than popular secondary structure prediction algorithms.
Boosting AlphaFold Protein Tertiary Structure Prediction through MSA Engineering and Extensive Model Sampling and Ranking in CASP16 https://www.biorxiv.org/content/10.1101/2025.06.06.658338v1
June 10, 2025 at 3:47 AM
Boosting AlphaFold Protein Tertiary Structure Prediction through MSA Engineering and Extensive Model Sampling and Ranking in CASP16 https://www.biorxiv.org/content/10.1101/2025.06.06.658338v1
Throughout the history of NA structure prediction, accuracy has been dependent on template availability, a trend that unfortunately continues in CASP16. Protein structure prediction has shown this is a surmountable challenge.
May 20, 2025 at 9:01 PM
Throughout the history of NA structure prediction, accuracy has been dependent on template availability, a trend that unfortunately continues in CASP16. Protein structure prediction has shown this is a surmountable challenge.
CASP16 protein monomer structure prediction assessment https://www.biorxiv.org/content/10.1101/2025.05.29.656942v1
June 2, 2025 at 6:48 PM
CASP16 protein monomer structure prediction assessment https://www.biorxiv.org/content/10.1101/2025.05.29.656942v1
This study evaluated the accuracy of nucleic acid structure predictions submitted to the CASP16 blind challenge.
November 13, 2025 at 1:23 AM
This study evaluated the accuracy of nucleic acid structure predictions submitted to the CASP16 blind challenge.
@peterskrinjar.bsky.social presenting #CAMEO and #PLINDER at #CASP16 , i.e what we at the @torstenschwede.bsky.social group have been up to since last CASP in automating benchmarking of complex prediction.
December 1, 2024 at 11:04 PM
@peterskrinjar.bsky.social presenting #CAMEO and #PLINDER at #CASP16 , i.e what we at the @torstenschwede.bsky.social group have been up to since last CASP in automating benchmarking of complex prediction.
Martini and Calvados used for flexible predictions in #casp16 by @lindorfflarsen.bsky.social
December 4, 2024 at 3:23 PM
Martini and Calvados used for flexible predictions in #casp16 by @lindorfflarsen.bsky.social
CASP16 protein monomer structure prediction assessment https://www.biorxiv.org/content/10.1101/2025.05.29.656942v1
June 2, 2025 at 6:48 PM
CASP16 protein monomer structure prediction assessment https://www.biorxiv.org/content/10.1101/2025.05.29.656942v1
It was great to be involved in the evaluation of nucleic acid structure prediction in CASP16! 🧬
RNA modeling remains challenging for deep learning, esp. in the absence of templates and for long-range tertiary/quaternary interactions. Encouraging signs from deep evolutionary data though.
RNA modeling remains challenging for deep learning, esp. in the absence of templates and for long-range tertiary/quaternary interactions. Encouraging signs from deep evolutionary data though.
Assessment of nucleic acid structure prediction in CASP16
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...
www.biorxiv.org
May 14, 2025 at 3:32 AM
It was great to be involved in the evaluation of nucleic acid structure prediction in CASP16! 🧬
RNA modeling remains challenging for deep learning, esp. in the absence of templates and for long-range tertiary/quaternary interactions. Encouraging signs from deep evolutionary data though.
RNA modeling remains challenging for deep learning, esp. in the absence of templates and for long-range tertiary/quaternary interactions. Encouraging signs from deep evolutionary data though.
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers pubmed.ncbi.nlm.nih.gov/40905273/ #cryoem
September 5, 2025 at 6:41 PM
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers pubmed.ncbi.nlm.nih.gov/40905273/ #cryoem
Modeling Alternative Conformational States in CASP16 www.biorxiv.org/content/10.1101/2025.09.02.673835v1 #cryoem
September 3, 2025 at 7:10 AM
Modeling Alternative Conformational States in CASP16 www.biorxiv.org/content/10.1101/2025.09.02.673835v1 #cryoem
“The assessment of monomer targets in the Critical Assessment of Structure Prediction Round 16 (CASP16) underscores that the problem of single-domain protein fold prediction is nearly solved--no target folds were missed across all Evaluation Units.”
CASP16 protein monomer structure prediction assessment https://www.biorxiv.org/content/10.1101/2025.05.29.656942v1
June 2, 2025 at 8:42 PM
“The assessment of monomer targets in the Critical Assessment of Structure Prediction Round 16 (CASP16) underscores that the problem of single-domain protein fold prediction is nearly solved--no target folds were missed across all Evaluation Units.”
Assessment of Protein Complex Predictions in CASP16: Are we making progress? https://www.biorxiv.org/content/10.1101/2025.05.29.656875v1
May 30, 2025 at 7:48 PM
Assessment of Protein Complex Predictions in CASP16: Are we making progress? https://www.biorxiv.org/content/10.1101/2025.05.29.656875v1
@jeeberhardt.bsky.social presenting CASP16 PLI baselines. Big shout out to @jeremywohlwend.bsky.social and @gcorso.bsky.social for helping us with running Boltz-1 on short notice! Pretty weird results on autotaxin.
December 3, 2024 at 5:17 PM
@jeeberhardt.bsky.social presenting CASP16 PLI baselines. Big shout out to @jeremywohlwend.bsky.social and @gcorso.bsky.social for helping us with running Boltz-1 on short notice! Pretty weird results on autotaxin.
CAPRI conclusions from the CASP16 assembly session
December 2, 2024 at 4:26 PM
CAPRI conclusions from the CASP16 assembly session
In the CASP16 category examining modeling of multiple conformational states, "no one group dominated in these performance rankings across all targets." Server-based methods in particular were quite mediocre
Modeling Alternative Conformational States in CASP16
The CASP16 Ensemble Prediction experiment assessed advances in methods for modeling proteins, nucleic acids, and their complexes in multiple conformational states. Targets included systems with experi...
www.biorxiv.org
September 7, 2025 at 8:37 AM
In the CASP16 category examining modeling of multiple conformational states, "no one group dominated in these performance rankings across all targets." Server-based methods in particular were quite mediocre
Day 2 of the #CASP16 meeting starting with an opening keynote by John Jumper.
How did we come from AlphaFold1 to AlphaFold2?
www.nobelprize.org/prizes/chemi...
How did we come from AlphaFold1 to AlphaFold2?
www.nobelprize.org/prizes/chemi...
The Nobel Prize in Chemistry 2024
The Nobel Prize in Chemistry 2024 was divided, one half awarded to David Baker "for computational protein design", the other half jointly to Demis Hassabis and John Jumper "for protein structure predi...
www.nobelprize.org
December 2, 2024 at 12:51 PM
Day 2 of the #CASP16 meeting starting with an opening keynote by John Jumper.
How did we come from AlphaFold1 to AlphaFold2?
www.nobelprize.org/prizes/chemi...
How did we come from AlphaFold1 to AlphaFold2?
www.nobelprize.org/prizes/chemi...
Conclusion of RNA assessors in #CASP16 - we are still in the “template” phase. Prediction of nucleic acids structure is still challenging for targets without templates, often relying on intuition. No big leap in accuracy since CASP15. AI based methods have not (yet?) made a major difference.
December 3, 2024 at 1:30 PM
Conclusion of RNA assessors in #CASP16 - we are still in the “template” phase. Prediction of nucleic acids structure is still challenging for targets without templates, often relying on intuition. No big leap in accuracy since CASP15. AI based methods have not (yet?) made a major difference.
Next at #CASP16 - keynote by David Baker
“De novo protein design using deep learning”
www.nobelprize.org/prizes/chemi...
“De novo protein design using deep learning”
www.nobelprize.org/prizes/chemi...
The Nobel Prize in Chemistry 2024
The Nobel Prize in Chemistry 2024 was divided, one half awarded to David Baker "for computational protein design", the other half jointly to Demis Hassabis and John Jumper "for protein structure predi...
www.nobelprize.org
December 2, 2024 at 9:59 PM
Next at #CASP16 - keynote by David Baker
“De novo protein design using deep learning”
www.nobelprize.org/prizes/chemi...
“De novo protein design using deep learning”
www.nobelprize.org/prizes/chemi...