Google Scholar:
https://scholar.google.com/citations?user=4tGNjhQAAAAJ&hl=en&oi=ao
Rauscher Lab Publications
Haas-Neill, L., Joron, L., Lerner, E., Rauscher, S. (2025) PEG-mCherry interactions beyond classical macromolecular crowding. Protein Science 34, e5235. doi: 10.1002/pro.5235
Haas-Neill, L., Meneksedag-Erol, D., Chaudhry, A., Novoselova, M., Ashraf, Q.F., de Araujo, E.D., Wilson, D.J., Rauscher, S. (2025) The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain. Protein Science 34, e70022. doi: 10.1002/pro.70022
Lee, E., Rauscher, S. (2025) The conformational space of the SARS-CoV-2 main protease active site loops is determined by ligand binding and interprotomer allostery. Biochemistry 64, 32–46. doi: 10.1021/acs.biochem.4c00575
Klyshko, E., Kim, J. S., McGough, L., Valeeva, V., Lee, E., Ranganathan, R., Rauscher, S. (2024) Functional Protein Dynamics in a Crystal. Nature Communications 15, 3244. doi: 10.1038/s41467-024-47473-4
O’Mara, M. L., Rauscher, S., Wetmore, S. D. (2024) Introduction to the RSC Advances themed collection on “New insights into biomolecular systems from large-scale simulations” RSC Advances 14, 6985-6986. doi:10.1039/D4RA90012J
Joron, K., Oliveira Viegas, J., Haas-Neill, L., Bier, S., Drori, P., Dvir, S., Lin Lim, P. S., Rauscher, S., Meshorer, E., and Lerner E. (2023) Fluorescent protein lifetimes report increased local densities and phases of nuclear condensates during embryonic stem cell differentiation. Nature Communications 14, 4885. doi:10.1038/s41467-023-40647-6
Klyshko, E., Kim, J. S., Rauscher, S. (2023) LAWS: Local alignment for water sites — Tracking ordered water in simulations. Biophysical Journal 122, 2871-2883. doi:10.1016/j.bpj.2022.09.012
Armstrong, H. K., Bording-Jorgensen, M., Santer, D. M., Zhang, Z., Valcheva, R., Rieger, A. M., Kim, J. S., Dijk, S. I., Mahmood, R., Ogungbola, O., Jovel, J., Moreau, F., Gorman, H., Dickner, R., Jerasi, J., Mander,I. K., Lafleur, D., Cheng, C., Petrova, A., Jeanson, T. L., Mason, A., Sergi, C. M., Levine, A., Chadee, K., Armstrong, D., Rauscher, S., Bernstein, C. N., Carroll, M. W., Huynh, H. Q., Walter, J., Madsen, K. L., Dieleman, L. A., Wine, E. (2022) Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients. Gastroenterology (in press). doi:10.1053/j.gastro.2022.09.034
Jang, J., Reed, P. M. M., Rauscher, S., Woolley, G. A. (2022) Point (S-to-G) Mutations in the W (S/G) GE Motif in Red/Green Cyanobacteriochrome GAF Domains Enhance Thermal Reversion Rates. Biochemistry 61, 1444-1455. doi:10.1021/acs.biochem.2c00060
Lazar, T., Guharoy, M., Vranken, W., Rauscher, S., Wodak, S. J., Tompa, P. (2020) Distance-based metrics for comparing conformational ensembles of intrinsically disordered proteins. Biophysical Journal 118, 2952-2965. doi:10.1101/2020.04.06.027979
de Araujo, E. D., Erdogan, F., Neubauer, H., Meneksedag-Erol, D., Manaswiyoungkul, P., Eram, M., Qadree, A., Israelian, J., Orlova, A., Seo, H. S., Suske, T., Pham, H. T. T., Boersma, A., Tangermann, S., Kenner, L., Rulicke, T., Dong, A., Ravichandran, M., Brown, P., Audette, G., Rauscher, S., Dhe- Paganon, S., Moriggl, R., Gunning, P. T. (2019) Structural and Functional Consequences of the STAT5B N642H Driver Mutation. Nature Communications 10, 1-15. doi:10.1038/s41467-019-10422-7
Meneksedag-Erol D., Rauscher S. (2019) Atomistic Simulation Tools to Study Protein Self-Aggregation. In Protein Self-Assembly. Methods in Molecular Biology, vol 2039. edited by Jennifer McManus, Springer/Humana, New York, NY, p. 243-262. doi:10.1007/978-1-4939-9678-0_17
Bandyopadhyay A., Van Eps N., Eger B., Rauscher S., Yedidi R., Moroni T., West G., Robinson K., Griffin P., Mitchell J., Ernst O. (2018) A Novel Polar Core and Weakly Fixed C-Tail in Squid Arrestin Provide New Insight into Interaction with Rhodopsin. Journal of Molecular Biology 430, 4102-4118. doi: 10.1016/j.jmb.2018.08.009
Publications pre-2017
Rauscher, S., Pomès, R. (2017) The Liquid Structure of Elastin. eLife 6, e26526. doi:10.7554/eLife.26526
Huang, J., Rauscher, S., Nawrocki, G., Ran,T., Feig, M., de Groot, B. L., Grubmüller, H., MacKerell Jr., A. D. (2017) CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nature Methods 14, 71-73 doi:10.1038/ NMETH.4067
Rauscher, S., Gapsys, V., Gajda, M. J., Zweckstetter, M., de Groot, B. L., Grubmüller, H. (2015) Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment. Journal of Chemical theory and Computation 11, 5513−5524. doi: 10.1021/acs.jctc.5b00736
Naqvi, A., Rauscher, S., Rousseau, D., Pomès, R. (2014) e Conformational Ensemble of the β‐Casein Phosphopeptide Reveals Two Independent Intrinsically Disordered Segments. Biochemistry 53, 6402−6408. doi: 10.1021/bi500107u
Neale, C., Madill, C., Rauscher, S., Pomès, R. (2013) Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. Journal of Chemical theory and Computation 9, 3686–3703. doi: 10.1021/ct301005b
Rauscher, S., Pomès, R. Structural Disorder and Protein Elasticity. In Fuzziness: Structural Disorder in Protein Complexes, edited by Peter Tompa and Monika Fuxreiter. Austin/New York: Landes Bioscience/Springer Science & Business Media, 2012:159-183. doi: 10.1007/978-1-4614-0659-4_10.
Seo, M., Rauscher, S., Pomès, R., Tieleman, D. P. (2012) Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides. Journal of Chemical theory and Computation 8, 1774–1785. doi: 10.1021/ct200876v
Li, G., Rauscher, S., Baud, S., Pomès, R. (2012) Binding of Inositol Stereoisomers to Model Amyloidogenic Peptides. Journal of Physical Chemistry B 116, 1111-1119. doi: 10.1021/jp208567n
Nikolic, A., Baud, S., Rauscher, S., Pomès, R. (2011) Molecular mechanism of β- sheet self-organization at water-hydrophobic interfaces. Proteins 79, 1-22. doi: 10.1002/prot.22854
Rauscher, S., Pomès, R. (2010) Molecular Simulations of Protein Disorder. Biochemistry and Cell Biology 88, 269-290. doi: 10.1139/o09-169
Rauscher, S., Pomès, R. (2010) Simulated Tempering Distributed Replica Sampling: A Practical Guide to Enhanced Conformational Sampling. Journal of Physics: Conference Series 256, 012011. doi: 10.1088/1742-6596/256/1/012011
Rauscher, S., Neale, C., Pomès, R. (2009) Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling. Journal of Chemical Theory and Computation 5, 2640-2662. doi: 10.1021/ct900302n
Rauscher, S., Baud, S., Miao, M., Keeley, F. W., Pomès, R. (2006) Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. Structure 14, 1667-1676. doi: 10.1016/j.str.2006.09.008
Knapp, D., Kallin, C., Ghosal, A., Mansour, S. (2005) Antiferromagnetism and charged vortices in high-Tc superconductors. Physical Review B 71, 064504. doi: 10.1103/PhysRevB.71.064504
Cozzolino, A. F., Vargas-Baca, I. Mansour, S., Mahmoudkhani, A. H. (2005) The Nature of the Supramolecular Association of 1,2,5-Chalcogenadiazoles. Journal of the American Chemical Society 9, 3184-3190. doi: 10.1021/ja044005y
Zhang, W., Cozzolino, A. F., Mahmoudkhani, A. H., Tulumello, M., Mansour, S.,Vargas-Baca, I. (2005) Influence of π-Stacking on the Resonant Enhancement of the Second-Order Nonlinear Optical Response of Dipolar Chromophores. Journal of Physical Chemistry B 109, 18378-18384. doi: 10.1021/jp053142u
Mahmoudkhani, A. H., Rauscher, S., Grajales, B., Vargas-Baca, I. (2003) Structural Diversity of Lithium Sulfenamides: 7Li NMR Studies in Solution and Crystal Structures of [Li2(η2-(CH3)3C-NS-C6H4CH3-4)2(THF)2] and [Li2(η1-4-CH3C6H4-NS-C6H4CH3-4)2(THF)4]. Inorganic Chemistry 42, 3849-3855. doi: 10.1021/ic026269w