Celeste Sagui

Fakharzadeh, A., Zhang, J., Roland, C., & Sagui, C. (2022, May 10). Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. NUCLEIC ACIDS RESEARCH. https://doi.org/10.1093/nar/gkac339

Zhang, J., Fakharzadeh, A., Pan, F., Roland, C., & Sagui, C. (2021). Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats. BIO-PROTOCOL. https://doi.org/10.21769/BioProtoc.4155

Pan, F., Zhang, Y., Xu, P., Man, V. H., Roland, C., Weninger, K., & Sagui, C. (2021). [Review of Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. https://doi.org/10.1016/j.csbj.2021.04.037

Tran, T. T., Pan, F., Tran, L., Roland, C., & Sagui, C. (2021). The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer. RSC ADVANCES, 11(5), 2664–2676. https://doi.org/10.1039/d0ra08837d

Zhang, J., Fakharzadeh, A., Pan, F., Roland, C., & Sagui, C. (2020). Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids. NUCLEIC ACIDS RESEARCH, 48(17), 9899–9917. https://doi.org/10.1093/nar/gkaa665

Pan, F., Zhang, Y., Man, V. H., Roland, C., & Sagui, C. (2018). E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats. Nucleic Acids Research, 46(2), 942–955. https://doi.org/10.1093/nar/gkx1186

Zhang, Y., Roland, C., & Sagui, C. (2018). Structural and dynamical characterization of DNA and RNA quadruplexes obtained from the GGGGCC and GGGCCT hexanucleotide repeats associated with C9FTD/ALS and SCA36 diseases. ACS Chemical Neuroscience, 9(5), 1104–1117. https://doi.org/10.1021/acschemneuro.7b00476

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2018). Structure and dynamics of DNA and RNA double helices obtained from the CCG and GGC trinucleotide repeats. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 122(16), 4491–4512. https://doi.org/10.1021/acs.jpcb.8b01658

Zhang, Y., Roland, C., & Sagui, C. (2017). Structure and dynamics of DNA and RNA double helices obtained from the GGGGCC and CCCCGG hexanucleotide repeats that are the hallmark of C9FTD/ALS diseases. ACS Chemical Neuroscience, 8(3), 578–591. https://doi.org/10.1021/acschemneuro.6b00348

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2017). Structure and dynamics of DNA and RNA double helices of CAG and GAC trinucleotide repeats. Biophysical Journal, 113(1), 19–36. https://doi.org/10.1016/j.bpj.2017.05.041

Zhang, Y., Man, V. H., Roland, C., & Sagui, C. (2016). Amyloid properties of asparagine and glutamine in prion-like proteins. ACS Chemical Neuroscience, 7(5), 576–587. https://doi.org/10.1021/acschemneuro.5b00337

Man, V. H., Pan, F., Sagui, C., & Roland, C. (2016). Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse. Journal of Chemical Physics, 144(14). https://doi.org/10.1063/1.4945340

Zhang, Y., Hoang Man, V., Roland, C., & Sagui, C. (2016). Contrasting Roles of Asparagine and Glutamine in the Aggregation of Prion-Like Proteins. Biophysical Journal, 110(3), 214a–215a. https://doi.org/10.1016/J.BPJ.2015.11.1191

Man, V. H., Van-Oanh, N. T., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2016). Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses. Physical Chemistry Chemical Physics, 18(17), 11951–11958. https://doi.org/10.1039/c5cp07711g

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2016). Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study. Biophysical Journal, 110(3), 407a. https://doi.org/10.1016/J.BPJ.2015.11.2197

Man, V. H., Roland, C., & Sagui, C. (2016). Structural Determinants of Polyqlutamine Protofibrils and Crystallites. Biophysical Journal, 110(3), 215a. https://doi.org/10.1016/J.BPJ.2015.11.1192

Moradi, M., Sagui, C., & Roland, C. (2015). Calculating transition and reaction rates with nonequilibrium work measurements. Xxvi iupap conference on computational physics (ccp2014), 640. https://doi.org/10.1088/1742-6596/640/1/012014

Viet, M. H., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2015). Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. Journal of Chemical Physics, 143(15). https://doi.org/10.1063/1.4933207

Viet, M. H., Truong, P. M., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2015). Picosecond melting of peptide nanotubes using an infrared laser: A nonequilibrium simulation study. Physical Chemistry Chemical Physics, 17(41), 27275–27280. https://doi.org/10.1039/c5cp04401d

Zhang, Y., & Sagui, C. (2015). Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI. Journal of Molecular Graphics & Modelling, 55, 72–84. https://doi.org/10.1016/j.jmgm.2014.10.005

Man, V. H., Roland, C., & Sagui, C. (2015). Structural determinants of polyglutamine protofibrils and crystallites. ACS Chemical Neuroscience, 6(4), 632–645. https://doi.org/10.1021/cn500358g

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2015). The adaptively biased molecular dynamics method revisited: New capabilities and an application. Xxvi iupap conference on computational physics (ccp2014), 640. https://doi.org/10.1088/1742-6596/640/1/012020

Cisneros, G. A., Karttunen, M., Ren, P. Y., & Sagui, C. (2014). [Review of Classical electrostatics for biomolecular simulations]. Chemical Reviews, 114(1), 779–814. https://doi.org/10.1021/cr300461d

Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2014). Correction to Classical Electrostatics for Biomolecular Simulations. Chemical Reviews, 114(9), 5116–5116. https://doi.org/10.1021/CR500124K

Moradi, M., Sagui, C., & Roland, C. (2014). Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities. The Journal of Chemical Physics, 140(3), 034114. https://doi.org/10.1063/1.4861055

Moradi, M., Sagui, C., & Roland, C. (2014). Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014). Journal of Chemical Physics, Vol. 140. https://doi.org/10.1063/1.4865580

Moradi, M., Sagui, C., & Roland, C. (2014). Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates. The Journal of Chemical Physics, 140(3), 034115. https://doi.org/10.1063/1.4861056

Moradi, M., Sagui, C., & Roland, C. (2014). Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014). Journal of Chemical Physics, Vol. 140. https://doi.org/10.1063/1.4865582

Pan, F., Roland, C., & Sagui, C. (2014). Ion distributions around left- and right-handed DNA and RNA duplexes: A comparative study. Nucleic Acids Research, 42(22), 13981–13996. https://doi.org/10.1093/nar/gku1107

Zhang, Y., & Sagui, C. (2014). The gp41(659-671) HIV-1 antibody epitope: A structurally challenging small peptide. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 118(1), 69–80. https://doi.org/10.1021/jp409355r

Babin, V., Wang, D. L., Rose, R. B., & Sagui, C. (2013). Binding polymorphism in the DNA bound state of the Pdx1 Homeodomain. PLoS Computational Biology, 9(8). https://doi.org/10.1371/journal.pcbi.1003160

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2013). Reaction path ensemble of the B-Z-DNA transition: A comprehensive atomistic study. Nucleic Acids Research, 41(1), 33–43. https://doi.org/10.1093/nar/gks1003

Moradi, M., Babin, V., Sagui, C., & Roland, C. (2011). A Statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides. Biophysical Journal, 100(4), 1083–1093. https://doi.org/10.1016/j.bpj.2010.12.3742

Moradi, M., Sagui, C., & Roland, C. (2011). Calculating relative transition rates with driven nonequilibrium simulations. Chemical Physics Letters, 518, 109–113. https://doi.org/10.1016/j.cplett.2011.10.054

Moradi, M., Babin, V., Sagui, C., & Roland, C. (2011). PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment. The Journal of Physical Chemistry B, 115(26), 8645–8656. https://doi.org/10.1021/jp203874f

Babin, V., Roland, C., & Sagui, C. (2011). The alpha-sheet: A missing-in-action secondary structure? Proteins, 79(3), 937–946. https://doi.org/10.1002/prot.22935

Moradi, M., Babin, V., Roland, C., & Saguia, C. (2010). A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. Journal of Chemical Physics, 133(12). https://doi.org/10.1063/1.3481087

Babin, V., & Sagui, C. (2010). Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water. Journal of Chemical Physics, 132(10). https://doi.org/10.1063/1.3355621

Lee, J.-G., Sagui, C., & Roland, C. (2010). Dimerization free energy of vancomycin-group antibiotics and the cooperative effect: A density functional approach. International Journal of Quantum Chemistry, 110(15), 2894–2902. https://doi.org/10.1002/qua.22926

Moradi, M., Lee, J.-G., Babin, V., Roland, C., & Sagui, C. (2010). Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation. International Journal of Quantum Chemistry, 110(15), 2865–2879. https://doi.org/10.1002/qua.22875

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009). Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential. International Journal of Quantum Chemistry, 109(15), 3666–3678. https://doi.org/10.1002/qua.22413

Moradi, M., Babin, V., Roland, C., Darden, T. A., & Sagui, C. (2009). Conformations and free energy landscapes of polyproline peptides. Proceedings of the National Academy of Sciences of the United States of America, 106(49), 20746–20751. https://doi.org/10.1073/pnas.0906500106

Babin, V., Roland, C., & Sagui, C. (2008). Adaptively biased molecular dynamics for free energy calculations. Journal of Chemical Physics, 128(13). https://doi.org/10.1063/1.2844595

Luo, X., Qian, G. F., Sagui, C., & Roland, C. (2008). Amino acid adsorption on the Si(100) surface: The case of glycine. Journal of Physical Chemistry. C, 112(7), 2640–2648. https://doi.org/10.1021/jp0775193

Karttunen, M., Rottler, J., Vattulainen, I., & Sagui, C. (2008). [Review of Electrostatics in biomolecular simulations: Where are we now and where are we heading?]. Computational modeling of membrane bilayers, 60, 49–89. https://doi.org/10.1016/s1063-5823(08)00002-1

Odbadrakh, K., Luo, X., Lee, J. G., Sagui, C., & Roland, C. (2007). Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces. Journal of Physical Chemistry. C, 111(34), 12760–12767. https://doi.org/10.1021/jp073042j

Lee, J. G., Asciutto, E., Babin, V., Sagui, C., Darden, T., & Roland, C. (2006). Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 110(5), 2325–2331. https://doi.org/10.1021/jp055809i

Babin, V., Baucom, J., Darden, T. A., & Sagui, C. (2006). Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 110(23), 11571–11581. https://doi.org/10.1021/jp061421r

Babin, V., Baucom, J., Darden, T. A., & Sagui, C. (2006). Molecular dynamics simulations of polarizable DNA in crystal environment. International Journal of Quantum Chemistry, 106(15), 3260–3269. https://doi.org/10.1002/qua.21152

Babin, V., Roland, C., Darden, T. A., & Sagui, C. (2006). The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. Journal of Chemical Physics, 125(20). https://doi.org/10.1063/1.2393236

Asciutto, E., & Sagui, C. (2005). Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions. Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment & General Theory, 109(34), 7682–7687. https://doi.org/10.1021/jp053428z

Sagui, C., Asciutto, E., & Roland, C. (2005). New and exotic self-organized patterns for modulated nanoscale systems. Nano Letters, 5(2), 389–395. https://doi.org/10.1021/nl048224t

Lee, J. G., Sagui, C., & Roland, C. (2005). Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 109(43), 20588–20596. https://doi.org/10.1021/jp0548117

Asciutto, E., Roland, C., & Sagui, C. (2005). Self-assembled patterns and strain-induced instabilities for modulated systems. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 72(2). https://doi.org/10.1103/physreve.72.021504

Herce, D. H., Perera, L., Darden, T. A., & Sagui, C. (2005). Surface solvation for an ion in a water cluster. Journal of Chemical Physics, 122(2). https://doi.org/10.1063/1.1829635

Sagui, C., Pomorski, P., Darden, T. A., & Roland, C. (2004). Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations. Journal of Chemical Physics, 120(9), 4530–4544. https://doi.org/10.1063/1.1644800

Lee, J. G., Sagui, C., & Roland, C. (2004). First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini. Journal of the American Chemical Society, 126(27), 8384–8385. https://doi.org/10.1021/ja048645c

Baucom, J., Transue, T., Fuentes-Cabrera, M., Krahn, J. M., Darden, T. A., & Sagui, C. (2004). Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields. Journal of Chemical Physics, 121(14), 6998–7008. https://doi.org/10.1063/1.1788631

Sagui, C., Pedersen, L. G., & Darden, T. A. (2004). Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations. Journal of Chemical Physics, 120(1), 73–87. https://doi.org/10.1063/1.1630791

Herce, H. D., Darden, T., & Sagui, C. (2003). Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles. Journal of Chemical Physics, 119(15), 7621–7632. https://doi.org/10.1063/1.1609191

Somoza, A. M., Sagui, C., & Roland, C. (2001). Liquid-crystal phases of capped carbon nanotubes - art. no.081403. Physical Review. B, Condensed Matter and Materials Physics, 6308(8), 1403. https://doi.org/10.1103/physrevb.63.081403