51����

Wissam Karroucha,��Carlos Oliver,��Véronique Stoven,��Vincent Mallet
J. Chem. Inf. Model. 27 July 2026; 66 (14): 7840-7861. https://doi.org/10.1021/acs.jcim.6c01094

Stephanie A. Wankowicz, Massimiliano Bonomi
Nature Methods

Tang Q, Wu T, Soubasis B,��Mchaourab HS.
bioRxiv [Preprint]. 2026 Feb 20:2026.02.19.706864. doi: 10.64898/2026.02.19.706864.

Shi, Kaiwen, and Carlos Oliver.
"ENSEMBITS: an alphabet of protein conformational ensembles." arXiv preprint arXiv:2605.13789��(2026).

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Juan G. Carvajal-Patiño,��Vincent Mallet,��David Becerra,��Luis Fernando Niño Vasquez,��Carlos Oliver��&��Jérôme Waldispühl
Nature Communications

Benjamin P. Brown
PNAS

Carvajal-Patiño JG, Mallet V, Becerra D, Niño Vasquez LF, Oliver C, Waldispühl J
Nature Communications

Wu T, Stein RA, Kao TY, Brown B,��Mchaourab HS.
Nat Commun. 2025 51���� Aug 2;16(1):7107. doi: 10.1038/s41467-025-62582-4.PMID:��40753333

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.

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.

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.

Wankowicz SA*, Ravikumar A, Sharma S, Riley BT, Raju A, van den Beden H, Keedy DA, Fraser JS.
eLife.

Wankowicz SA*, Fraser JS.
IUCrJ

Wankowicz SA, Beltrao P, Cravatt B, Dunbrack R, Gitter A, Lindorff-Larsen K, Ovchinnikov S, Polizzi N, Shoichet B, Fraser JS.
Zenodo Preprint.

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.

Stein RA, Mchaourab HS.
bioRxiv [Preprint]. 2024 Jan 27:2023.09.05.556364. doi: 10.1101/2023.09.05.556364. PMID: 37732281; PMCID:
PMC10508732.

Sinclair M, Stein RA, Sheehan J, Hawes EM, O’Brien RM, Tajkhorshid E, Claxton DP.
PNAS Nexus, 3, 036, 2024.

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.

Du S, Wankowicz SA, Yabukarski F, Doukov T, Hershlag, Fraser JS.
Methods in Enzymology.

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.

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.

Wankowicz SA, de Oliveira SHP, Hogan DW, van den Bedem H, Fraser JS.
eLife.

Stein RA, Mchaourab HS.
PLoS Comput Biol. 2022 Aug 22;18(8):e1010483. doi: 10.1371/journal.pcbi.1010483. PMID: 35994486; PMCID:
PMC9436118.

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.

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.

Del Alamo D, Sala D, Mchaourab HS, Meiler J.
Elife. 2022 Mar 3;11:e75751. doi: 10.7554/eLife.75751. PMID: 35238773; PMCID: PMC9023059.

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

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.

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.