From possibility to precision in macromolecular ensemble prediction
Stephanie A. Wankowicz, Massimiliano Bonomi
Nature Methods
Prediction of ligand-dependent conformational sampling of ABC transporters by AlphaFold3 and correlation to experimental structures and energetics
bioRxiv [Preprint]. 2026 Feb 20:2026.02.19.706864. doi: 10.64898/2026.02.19.706864.
ENSEMBITS: an alphabet of protein conformational ensembles
Shi, Kaiwen, and Carlos Oliver.
"ENSEMBITS: an alphabet of protein conformational ensembles." arXiv preprint arXiv:2605.13789 (2026).
RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.
Juan G. Carvajal-Patiño, Vincent Mallet, David Becerra, Luis Fernando Niño Vasquez, Carlos Oliver & Jérôme Waldispühl
Nature Communications
A generalizable deep learning framework for structure-based protein-ligand affinity ranking
Benjamin P. Brown
PNAS
RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning
Carvajal-Patiño JG, Mallet V, Becerra D, Niño Vasquez LF, Oliver C, Waldispühl J
Nature Communications
Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions
Nat Commun. 2025 Aug 2;16(1):7107. doi: 10.1038/s41467-025-62582-4.PMID: 40753333
Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.
Alexandra C Schwartz, Richard A Stein, Eva Gil-Iturbe, Matthias Quick, Hassane S Mchaourab.
PNAS
Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.
Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo A, van den Bedem H, Fraser J, Wankowicz SA.*
BioRxiv.
Dynamic allostery drives autocrine and paracrine TGF-β signaling.
Jin M, Seed RI, Cai G, Shing T, Wang L, Ito S, Cormier A, Wankowicz SA, Jespersen JM, Baron JL, Carey ND, Campbell MG, Yu Z, Tang PK, Cossio P, Wen W, Lou J, Marks J, Nishimura SL, Cheng Y.
Cell.
A renewed call for open artificial intelligence in biomedicine.
Gitter A, Fraser JS, Gonen T, Patro R, Wayment-Steele HK, Williams A, Haibe-Kains B, Dunbrack RL, Cook C, Kundaje A, Hoffman MM, Carpenter AE, Wankowicz SA, Lindorff-Larsen K.
OSF Preprints.
Automated Multiconformer Building in X-ray Crystallography and CryoEM.
Wankowicz SA*, Ravikumar A, Sharma S, Riley BT, Raju A, van den Beden H, Keedy DA, Fraser JS.
eLife.
Comprehensive Encoding of Conformational and Compositional Protein Structural Ensembles through mmCIF Data Structure.
Wankowicz SA*, Fraser JS.
IUCrJ
AlphaFold3 Transparency and Reproducibility.
Wankowicz SA, Beltrao P, Cravatt B, Dunbrack R, Gitter A, Lindorff-Larsen K, Ovchinnikov S, Polizzi N, Shoichet B, Fraser JS.
Zenodo Preprint.
Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.
Brown BP, Stein RA, Meiler J, Mchaourab HS.
J Chem Theory Comput. 2024 Feb 13;20(3):1434-1447. doi: 10.1021/acs.jctc.3c01081. Epub 2024 Jan 12. PMID:
38215214; PMCID: PMC10867840.
Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles.
Stein RA, Mchaourab HS.
bioRxiv [Preprint]. 2024 Jan 27:2023.09.05.556364. doi: 10.1101/2023.09.05.556364. PMID: 37732281; PMCID:
PMC10508732.
Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model.
Sinclair M, Stein RA, Sheehan J, Hawes EM, O’Brien RM, Tajkhorshid E, Claxton DP.
PNAS Nexus, 3, 036, 2024.
Computer-aided design and biological evaluation of diazaspirocyclic D4R antagonists.
Jones, C.A.H.†, Brown, B.P., Schultz, D.C.*, Engers, J., Kramlinger, V.M., Meiler, J.†, Lindsley, C.†
Computer-aided design and biological evaluation of diazaspirocyclic D4R antagonists.
ACS Chemical Neuroscience.
Advances in uncovering the mechanisms of macromolecular conformational entropy.
Wankowicz SA*, Fraser JS.
Nature Chemical Biology.
Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data.
Du S, Wankowicz SA, Yabukarski F, Doukov T, Hershlag, Fraser JS.
Methods in Enzymology.
Modeling conformational states of proteins with AlphaFold.
Sala D, Engelberger F, Mchaourab HS, Meiler J.
Curr Opin Struct Biol. 2023 Aug;81:102645. doi: 10.1016/j.sbi.2023.102645. Epub 2023 Jun 29. PMID: 37392556.
Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2.
Gulsevin A, Han B, Porta JC, Mchaourab HS, Meiler J, Kenworthy AK.
Biophys J. 2023 Jun 6;122(11):2041-2052. doi: 10.1016/j.bpj.2022.11.011. Epub 2022 Nov 9. PMID: 36352786; PMCID: PMC10257013.
Ligand binding remodels protein side chain conformational heterogeneity.
Wankowicz SA, de Oliveira SHP, Hogan DW, van den Bedem H, Fraser JS.
eLife.
SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2.
Stein RA, Mchaourab HS.
PLoS Comput Biol. 2022 Aug 22;18(8):e1010483. doi: 10.1371/journal.pcbi.1010483. PMID: 35994486; PMCID:
PMC9436118.
Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter.
Del Alamo D, DeSousa L, Nair RM, Rahman S, Meiler J, Mchaourab HS.
Proc Natl Acad Sci U S A. 2022 Aug 23;119(34):e2206129119. doi: 10.1073/pnas.2206129119. Epub 2022 Aug 15. PMID: 35969794; PMCID: PMC9407458.
Modeling of protein conformational changes with Rosetta guided by limited experimental data.
Sala D, Del Alamo D, Mchaourab HS, Meiler J.
Structure. 2022 Aug 4;30(8):1157-1168.e3. doi: 10.1016/j.str.2022.04.013. Epub 2022 May 20. PMID: 35597243; PMCID: PMC9357069.
Sampling alternative conformational states of transporters and receptors with AlphaFold2.
Del Alamo D, Sala D, Mchaourab HS, Meiler J.
Elife. 2022 Mar 3;11:e75751. doi: 10.7554/eLife.75751. PMID: 35238773; PMCID: PMC9023059.
Allele-specific activation, enzyme kinetics, and inhibitor sensitivities among EGFR exon 19 deletions in lung adenocarcinoma.
Brown, B.P.* †, Zhang, Y.*, Kim, S.*, Finneran, P., Du, Z., Yan, Y., Smith, A.W. †, Lovly, C.M. † , Meiler, J. †
Proceedings of the National Academy of Sciences of the United States of America. *Equally contributing co-first authors †Co-corresponding authors
General purpose structure-based drug discovery neural network score functions with human interpretable pharmacophore maps.
Brown, B.P. †, Mendenhall, J., Geanes, A.R., Meiler, J†.
Journal of Chemical Information and Modeling. †Co-corresponding authors Sample dynamics papers, mostly EGFR/ErbB structure prediction + dynamics.
Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity.
Hanker, A.B.*, Brown, B.P.*, Meiler, J.*, Marín, A., Harikrishna, S., Ye, D., Lin, C., Akamatsu, H., Lee, K., Chatterjee, S., Sudhan, D.R., Servetto, A., Red-Brewer, M., Koch, J.P., Sheehan, J.H., He, J., Lalani, A.S., Arteaga, C.L.
Cancer Cell.