Celeste Sagui Code, C., Qiu, D., Solov'yov, I. A., Lee, J.-G., Shin, H.-C., Roland, C., … Jorgensen, T. J. D. (2023, October 26). Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. https://doi.org/10.1021/jacs.3c04068 Xu, P., Zhang, J., Pan, F., Mahn, C., Roland, C., Sagui, C., & Weninger, K. (2023). Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity. JOURNAL OF MOLECULAR BIOLOGY, 435(10). https://doi.org/10.1016/j.jmb.2023.168086 Kandola, T., Venkatesan, S., Zhang, J., Lerbakken, B. T., Von Schulze, A., Blanck, J. F., … Halfmann, R. (2023). Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. ELIFE, 12. https://doi.org/10.7554/eLife.86939 Fakharzadeh, A., Qu, J., Pan, F., Sagui, C., & Roland, C. (2023, September 8). Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids. JOURNAL OF PHYSICAL CHEMISTRY B. https://doi.org/10.1021/acs.jpcb.3c03538 Man, V. H., He, X., Nguyen, P. H., Sagui, C., Roland, C., Xie, X.-Q., & Wang, J. (2023). Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation. COMPUTERS IN BIOLOGY AND MEDICINE, 159. https://doi.org/10.1016/j.compbiomed.2023.106902 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., Roland, C., & Sagui, C. (2022). RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences. ACS OMEGA, 7(43), 38728–38743. https://doi.org/10.1021/acsomega.2c04358 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, 11(18). 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, 19, 2819–2832. 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, 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), Vol. 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), Vol. 640. https://doi.org/10.1088/1742-6596/640/1/012020 Cisneros, G. A., Karttunen, M., Ren, P., & 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, February 14). 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, February 14). 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, 118(1), 69–80. https://doi.org/10.1021/jp409355r Babin, V., Wang, D., 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 α-sheet: A missing-in-action secondary structure? Proteins: Structure, Function, and Bioinformatics, 79(3), 937–946. https://doi.org/10.1002/prot.22935 Moradi, M., Babin, V., Roland, C., & Sagui, 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, December). Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 109, pp. 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., 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). Electrostatics in biomolecular simulations: Where are we now and where are we heading? COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, Vol. 60, pp. 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, 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, 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, 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, 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, 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. PHYSICAL REVIEW B, 63(8). https://doi.org/10.1103/physrevb.63.081403