Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15
Open accessPreprint — published as 10.1002/prot.26584 · Paper page
Abstract
For the first time, the 2022 CASP (Critical Assessment of Structure Prediction) community experiment included a section on computing multiple conformations for protein and RNA structures. There was full or partial success in reproducing the ensembles for four of the nine targets, an encouraging result. For protein structures, enhanced sampling with variations of the AlphaFold2 deep learning method was by far the most effective approach. One substantial conformational change caused by a single mutation across a complex interface was accurately reproduced. In two other assembly modeling cases, methods succeeded in sampling conformations near to the experimental ones even though environmental factors were not included in the calculations. An experimentally derived flexibility ensemble allowed a single accurate RNA structure model to be identified. Difficulties included how to handle sparse or low-resolution experimental data and the current lack of effective methods for modeling RNA/protein complexes. However, these and other obstacles appear addressable.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
LGA: a method for finding 3D similarities in protein structures
Zemla, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg571 · Cited by 1,069 · see citing works
Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · see citing works
Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp>
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26237 · Cited by 503 · see citing works
Self-citationHigh‐accuracy protein structure prediction in <scp>CASP14</scp>
Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26171 · Cited by 314 · see citing works
Self-citationConformational states dynamically populated by a kinase determine its function
Xie, T., Saleh, T., Rossi, P., & Kalodimos, C. G. (2020) · Science · doi:10.1126/science.abc2754 · Cited by 266 · see citing works
AlphaFold, Artificial Intelligence (AI), and Allostery
Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works
Modeling conformational states of proteins with AlphaFold
Sala, D., Engelberger, F., Mchaourab, H. S., & Meiler, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102645 · Cited by 182 · see citing works
Improving peptide-protein docking with AlphaFold-Multimer using forced sampling
Johansson-Åkhe, I., & Wallner, B. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.959160 · Cited by 162 · see citing works
Efficient and accurate prediction of protein structure using RoseTTAFold2Preprint
Baek, M., Anishchenko, I. V., Humphreys, I. R., Cong, Q., Baker, D. A., & DiMaio, F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.24.542179 · Cited by 152 · see citing works
Protein structure prediction has reached the single-structure frontier
Lane, T. J. (2023) · Nature Methods · doi:10.1038/s41592-022-01760-4 · Cited by 125 · see citing works
Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis
Dasgupta, M., Budday, D., de Oliveira, S. H. P., Madzelan, P., Marchany‐Rivera, D., Seravalli, J., Hayes, B., Sierra, R. G., Boutet, S., Hunter, M. S., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1901864116 · Cited by 87 · see citing works
Sala, D., Hildebrand, P. W., & Meiler, J. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1121962 · Cited by 80 · see citing works
Comparison of performance in successive CASP experiments
Venclovas, ?., Zemla, A. T., Fidelis, K. A., & Moult, J. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10053 · Cited by 78 · see citing works
Self-citationAssessment of protein assembly prediction in CASP12
Lafita, A., Bliven, S., Kryshtafovych, A., Bertoni, M., Monastyrskyy, B., Duarte, J. M., Schwede, T., & Capitani, G. (2017) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25408 · Cited by 72 · see citing works
Self-citationPrediction of multiple conformational states by combining sequence clustering with AlphaFold2Preprint
Wayment-Steele, H. K., Ovchinnikov, S., Colwell, L. J., & Kern, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.17.512570 · Cited by 66 · see citing works
Joseph, A. P., Lagerstedt, I. C., Patwardhan, A., Topf, M., & Winn, M. (2017) · Journal of Structural Biology · doi:10.1016/j.jsb.2017.05.007 · Cited by 57 · see citing works
New prediction categories in <scp>CASP15</scp>
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26515 · Cited by 54 · see citing works
Self-citationPseudomonas fluorescens isocyanide hydratase at 274 K G150A mutant
Wilson, M. A., Dasgupta, M., & Bedem, H. V. D. (2018) · Worldwide Protein Data Bank · doi:10.2210/pdb6ni5/pdb · Cited by 46 · see citing works
Allosteric regulation and inhibition of protein kinases
Mingione, V. R., Paung, Y., Outhwaite, I. R., & Seeliger, M. A. (2023) · Biochemical Society Transactions · doi:10.1042/bst20220940 · Cited by 45 · see citing works
Tertiary structure assessment at CASP15
Simpkin, A. J., Mesdaghi, S., Rodríguez, F. S., Elliott, L. G., Murphy, D., Kryshtafovych, A., Keegan, R. M., & Rigden, D. J. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26593 · Cited by 43 · see citing works
Self-citationRNA target highlights in CASP15: Evaluation of predicted models by structure providers
Kretsch, R., Andersen, E., Bujnicki, J., Chiu, W., Das, R., Luo, B., Masquida, B., McRae, E., Schroeder, G. M., Su, Z.-M., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26550 · Cited by 38 · see citing works
Self-citationMechanism of AAA+ ATPase-mediated RuvAB–Holliday junction branch migration
Wald, J., Fahrenkamp, D., Goessweiner‐Mohr, N., Lugmayr, W., Ciccarelli, L., Vesper, O., & Marlovits, T. C. (2022) · Nature · doi:10.1038/s41586-022-05121-1 · Cited by 31 · see citing works
Protein target highlights in CASP15 : Analysis of models by structure providers
Alexander, L. T., Durairaj, J., Kryshtafovych, A., Abriata, L. A., Bayo, Y., Bhabha, G., Breyton, C., Caulton, S. G., Chen, J., Degroux, S., et al. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26545 · Cited by 27 · see citing works
Self-citationCryo‐electron microscopy targets in CASP13: Overview and evaluation of results
Kryshtafovych, A., Malhotra, S., Monastyrskyy, B., Cragnolini, T., Joseph, A. P., Chiu, W., & Topf, M. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25817 · Cited by 21 · see citing works
Self-citationBadiee, S. A., Isu, U. H., Khodadadi, E., & Moradi, M. (2023) · Membranes · doi:10.3390/membranes13060568 · Cited by 19 · see citing works
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps
Mulvaney, T., Kretsch, R. C., Elliott, L. G., Beton, J. G., Kryshtafovych, A., Rigden, D. J., Das, R., & Topf, M. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26644 · Cited by 15 · see citing works
Self-citationCragnolini, T., Kryshtafovych, A., & Topf, M. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26216 · Cited by 10 · see citing works
Self-citationMix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysisPreprint
Dasgupta, M., Budday, D., de Oliveira, S. H. P., Madzelan, P., Marchany‐Rivera, D., Seravalli, J., Hayes, B., Sierra, R. G., Boutet, S., Hunter, M. S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/524751 · Cited by 7 · see citing works
Flagged first, then by citations
4 of the 34 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
AlphaFold predictions of fold-switched conformations are driven by structure memorization
Chakravarty, D., Schafer, J. W., Chen, E. A., Thole, J. F., Ronish, L. A., Lee, M., & Porter, L. L. (2024) · Nature Communications · doi:10.1038/s41467-024-51801-z · Cited by 159 · see citing works
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26617 · Cited by 148 · see citing works
Self-citationBeyond static structures: protein dynamic conformations modeling in the post-AlphaFold era
Cui, X., Ge, L., Chen, X., Lv, Z., Wang, S., Zhou, X., & Zhang, G. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf340 · Cited by 67 · see citing works
New prediction categories in <scp>CASP15</scp>
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26515 · Cited by 54 · see citing works
Self-citationEmerging frontiers in protein structure prediction following the AlphaFold revolution
Rennie, M. L., & Oliver, M. R. (2025) · Journal of The Royal Society Interface · doi:10.1098/rsif.2024.0886 · Cited by 27 · see citing works
Explaining Conformational Diversity in Protein Families through Molecular Motions
Lombard, V., Grudinin, S., & Laine, É. (2024) · Scientific Data · doi:10.1038/s41597-024-03524-5 · Cited by 19 · see citing works
Luo, D., Zhang, Y., Li, Y., Liu, Z., Wu, H., & Xue, W. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03731 · Cited by 15 · see citing works
<scp>AlphaFold3</scp> at <scp>CASP16</scp>
Elofsson, A. (2026) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.70044 · Cited by 24 · see citing works
Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem
McBride, A. C., Yu, F., Cheng, E. H., Mpouli, A., Soe, A. C., Hammel, M., Montelione, G. T., Oas, T. G., Tsutakawa, S. E., & Donald, B. R. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70062 · Cited by 14 · see citing works
Self-citationProgress and Bottlenecks for Deep Learning in Computational Structure Biology: CASP Round XVI
Kryshtafovych, A., Schwede, T. F., Topf, M., Fidelis, K. A., & Moult, J. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70076 · Cited by 12 · see citing works
Self-citationRaisinghani, N., Parikh, V., Foley, B., & Verkhivker, G. M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252312968 · Cited by 10 · see citing works
Breaking Evolution’s Ceiling: AI-Powered Protein Engineering
Jin, S., Wu, Q., Fu, G., Lu, D. X., Wang, F., Deng, L. F., & Nie, K. (2025) · Catalysts · doi:10.3390/catal15090842 · Cited by 11 · see citing works
A fully automated benchmarking suite to compare macromolecular complexes
Studer, G., Robin, X., Bienert, S., Durairaj, J., Škrinjar, P., Tauriello, G., Waterhouse, A. M., & Schwede, T. (2026) · Nature Methods · doi:10.1038/s41592-025-02973-z · Cited by 10 · see citing works
Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution
Hilser, V. J., Wrabl, J. O., Millard, C. E., Schmitz, A., Brantley, S. J., Pearce, M., Rehfus, J., Russo, M. M., & Voortman‐Sheetz, K. (2025) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-061824-104900 · Cited by 9 · see citing works
Modeling Alternative Conformational States in CASP16
Dube, N., Ramelot, T. A., Benavides, T. L., Huang, Y. J., Moult, J., Kryshtafovych, A., & Montelione, G. T. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70065 · Cited by 10 · see citing works
Self-citationRaisinghani, N., Alshahrani, M., Gupta, G., & Verkhivker, G. M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251810082 · Cited by 8 · see citing works
Morehead, A., Liu, J., Neupane, P., & Cheng, J. (2026) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2026.103247 · Cited by 8 · see citing works
Abriata, L. A. (2026) · Communications Biology · doi:10.1038/s42003-026-10112-3 · Cited by 5 · see citing works
Precise DNA base editing using AlphaFold3-based contact modelling
Meng, H., Lei, Z., Yan, Y., Wang, L., Zhang, S., Rao, X., Shao, C., Zhang, X., Chen, K., Yang, L., et al. (2026) · Nature · doi:10.1038/s41586-026-10794-z · Cited by 6 · see citing works
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16
Kretsch, R. C., Posani, E., Baulin, E. F., Bujnicki, J. M., Bussi, G., Cheatham, T. E., Chen, S., Elofsson, A., Farsani, M. A., Fisher, O. N., et al. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70079 · Cited by 6 · see citing works
Lopez-Mateos, D., Narang, K., & Yarov-Yarovoy, V. (2026) · Journal of General Physiology · doi:10.1085/jgp.202413705 · Cited by 5 · see citing works
Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XV
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2023) · doi:10.22541/au.169658651.11658182/v1 · Cited by 5 · see citing works
Self-citationUpdates to the CASP Infrastructure in 2024
Kryshtafovych, A., Miłostan, M., Lensink, M. F., Velankar, S. S., Bonvin, A. M. J. J., Moult, J., & Fidelis, K. A. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70042 · Cited by 5 · see citing works
Self-citationAlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residuesPreprint
Ge, L., Cui, X., Zhao, K., Zhou, X., Zhang, Y., & Zhang, G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.11.664327 · Cited by 4 · see citing works
Benavides, T. L., & Montelione, G. T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.19.613999 · Cited by 2 · see citing works
Self-citationTevenvirinae phages encode a family of LSm-like fold proteins
Kim, J., Tai, C., Livingston, N. K., Patterson-West, J., Stearns, O., Son, B., & Hinton, D. M. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.05.028 · Cited by 2 · see citing works
Exploring Protein Conformational Ensembles Using Evolutionary Conditional Diffusion
Cui, X., Ge, L., Yang, X., Li, X., Hou, D., Zhou, X., & Zhang, G. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01319 · Cited by 1 · see citing works
A Review of RNA Structure Prediction: Exploring the Potential of Computational Approaches
Tripathi, A., Dhanuka, R., & Singh, J. P. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2024.3509982 · Cited by 1 · see citing works
Raisinghani, N., Alshahrani, M., Gupta, G., Tian, H., Xiao, S., Tao, P., & Verkhivker, G. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.17.594786 · Cited by 1 · see citing works
Raisinghani, N., Parikh, V., Foley, B., & Verkhivker, G. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.04.621947
Machine Learning for Protein Structure Prediction and Design
Bell, D. R., & Chen, S. H. (2025) · Springer handbooks · doi:10.1007/978-3-031-81728-1_46
- Authors
- Kryshtafovych, A., Montelione, G., Rigden, D., Mesdaghi, S., Karaca, E., & Moult, J.
- Affiliations
- University of California, Davis (US)
- Rensselaer Polytechnic Institute (US)
- University of Liverpool (GB)
- Dokuz Eylül University (TR)
- Institute for Bioscience and Biotechnology Research (US)
- Corresponding author
- Moult, John
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2023-08-14
- Volume
- 91
- Issue
- 12
- Pages
- 1903-1911
- ISSN
- 0887-3585 (ISSN-L)
- PMC
- PMC10840738
- OpenAlex
- W4387893024
- Cited by
- 31
- References
- 34
- Citations by year
- 2026: 4 · 2025: 16 · 2024: 8 · 2023: 3
- FWCI
- 2.76
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- University Libraries (University of Maryland) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Digital Repository at the University of Maryland (University of Maryland College Park)
- Funders
- National Institutes of Health
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/S007105/1)
- National Institute of General Medical Sciences (GM141818, R35GM141818, R01GM100482)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- conformational ensembles, CASP15, AlphaFold2, enhanced sampling, protein structure prediction, RNA structure prediction, protein-RNA complex, protein-protein complex, protein flexibility
- MeSH terms
- Mutation, Protein Conformation, Proteins, RNA
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
