• Yan, C., Dodd, T., Yu, J., Leung, B., Xu, J., Oh, J., Wang, D. & Ivanov, I.* Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. (2021) Nature Communications, doi:10.1038/s41467-021-27295-4

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• Dodd, T., Yao, X., Hamelberg, D. & Ivanov I.* Subsets of adjacent nodes (SOAN): A fast method for computing suboptimal paths in protein dynamic networks. (2021) Molecular Physics, doi:10.1080/00268976.2021.1893847

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• Dodd, T., Botto, M., Paul, F., Leiro, R.F, Lamers, M.H., & Ivanov, I.* Defined path for conformational switching from polymerization to editing in a high-fidelity DNA polymerase. Nature Communications (2020), 11, 5379, doi:10.1038/s41467-020-19165-2

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• Tsutakawa, S.E., Tsai, C-L., Yan, C., Bralić, A., Chazin, W.J., Hamdan, S.M., Schärer, O.D., Ivanov, I. &Tainer, J.A. Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. DNA Repair (2020), doi:10.1016/j.dnarep.2020.102972

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• Qian, K., Yan, C., Su, H., Dang, T., Zhou, B., Wang, Z., Zhao, X., Ivanov, I. & Zheng, Y.G. Pharmacophore-based screening of diamidine small molecule inhibitors for protein arginine methyltransferases. RCS Medicinal Chemistry (2020), doi:10.1039/D0MD00259C

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• Yuan, Z., Schneider, S., Dodd, T., Riera, A., Bai, L., Yan, C., Ivanov, I.*, Stillman, B., Li, H., & Speck, C. Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proceedings of the National Academy of Sciences USA (2020), 117, 17747-17756, doi:10.1073/pnas.2006231117

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• Dodd, T., Yan, C., & Ivanov, I.* Simulation-based methods for model building and refinement in cryo-electron microscopy. Journal of Chemical Information and Modeling (2020) 60, 2470–2483, doi:10.1021/acs.jcim.0c00087

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• Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural & Molecular Biology (2019), 26, 397-406, doi:10.1038/s41594-019-0220-3 (recommended by Faculty of 1000 Prime, highlighted by the Oak Ridge Leadership Computing Facility)

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• Perumal, S.K.; Xu, X.; Yan, C.; Ivanov, I.* & Benkovic, S.J. Recognition of a key anchor residue by a conserved hydrophobic pocket ensures subunit interfaces integrity in DNA clamps. Journal of Molecular Biology (2019), doi:10.1016/j.jmb.2019.04.035

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• Carter, E.K.; Laughlin, S.; Dodd, T.; Wilson, W.D. & Ivanov, I* Small molecule binders recognize DNA microstructural variations via an induced fit mechanism Physical Chemistry Chemical Physics (2019) doi:10.1039/C8CP05537H

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• Han, Y.; Yan, C.; Fishbain, S.; Ivanov, I. & He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018), doi:10.1038/s41421-018-0044-z

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• Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I.* Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018), doi:10.1073/pnas.1803323115

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• Li, J. et al. Natural Product Micheliolide (MCL) Irreversibly Activates Pyruvate Kinase M2 and Suppresses Leukemia. (2018) Journal of Medicinal Chemistry doi:10.1021/acs.jmedchem.8b00241

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• Han, Y.; Yan, C.; Nguyen, K.; Jackobel, A.; Ivanov, I.; Knutson, B.A.; He, Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife (2017) 6, e27414, doi:10.7554/eLife.27414

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• Rashid F. et al. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. (2017) eLife 6, e21884, doi:10.7554/eLife.21884

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• Zhang, J., Qian, K., Yan, C., He, M., Jassim, B., Ivanov, I. & Zheng, Y. Discovery of decamidine as a new and potent PRMT1 inhibitor. Medicinal Chemistry Communications (2017) 8, 440-444, doi:10.1039/C6MD00573J

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• Laughlin S.; Carter E.K.; Ivanov, I* & Wilson, W.D. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Research (2017) 45, 1297-1306, doi:10.1093/nar/gkw1232

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• Kossmann, B.; Abdelmalak, M.; Lopez, S.; Tender, G.; Yan, C.; Pommier, Y.; Marchand, C. & Ivanov, I* Discovery of selective inhibitors of tyrosyl-DNA phosphodiesterase 2 by targeting the enzyme DNA-binding cleft. Bioorganic and Medicinal Chemistry Letters (2016) doi:10.1016/j.bmcl.2016.05.065

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• He, Y., Yan, C., Inouye, C., Fang, J., Tjian, R., Ivanov, I. & Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature (2016) 533, 359–365, doi:10.1038/nature17970

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• Turaga, R.C., Yin, L., Yang, J.J., Lee, H., Ivanov, I., Yan, C., Grossniklaus, H.E., Wang, S., Ma, C., Sun, L. & Liu, Z. Development of protein drug targeting integrin αvβ3 at a novel site by rational protein design. Nature Communications (2016), 7 , e11675 doi:10.1038/ncomms11675

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• Hudson, W.H., Kossmann, B., de Vera, I.M., Chuo, S.W., Weikum, E.A., Eick G., Thornton, J., Ivanov, I., Kojetin, D.J., & Ortlund, E.A Distal substitutions drive divergent DNA specificity among paralogous transcription factors through a subdivision of conformational space. Proceedings of the National Academy of Sciences USA (2016) 113, 326-331, doi:10.1073/pnas.1518960113

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• Xu, X., Yan, C., Kossmann, B. & Ivanov, I.* Secondary interaction interfaces with PCNA control conformational switching of DNA polymerase PolB from polymerization to editing. Journal of Physical Chemistry B (2016) doi:10.1021/acs.jpcb.6b02082

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• Musille, P. M., Kossmann, B., Kohn, J. A., Ivanov, I., & Ortlund E. A. Unexpected allosteric network contributes to LRH-1 co-regulator selectivity. Journal of Biological Chemistry (2016) 291, 1411-1426, doi:10.1074/jbc.M115.662874

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• Xu, X., Yan, C., Wohlhueter, R., & Ivanov I.* Integrative modeling of macromolecular assemblies from low to near-atomic resolution. Computational and Structural Biotechnology Journal (2015) 13, 492–503, doi:10.1016/j.csbj.2015.08.005

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• Brosey, C.A., Soss, S.E., Brooks, S., Yan, C., Ivanov, I., Dorai, K., & Chazin, W.J. Functional dynamics in RPA DNA binding and protein recruitment domains. Structure (2015) 23, 1028–1038, doi:10.1016/j.str.2015.04.008

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• Tsutakawa, S.E., Yan, C., Xu, X., Weinacht, C., Frudental, B., Zhuang, Z., Washington, M.T., Tainer, J.A. & Ivanov, I.* Structurally distinct ubiquitin- and SUMO-modified PCNA: Implications for their distinct roles in the DNA Damage response. Structure (2015) 23, 724–733, doi:10.1016/j.str.2015.02.008

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• Kossmann, B. & Ivanov, I.* Alkylpurine glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases. PLOS Computational Biology (2014) 10, e1003704. doi:10.1371/journal.pcbi.1003704

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• Yan, L., Yan, C., Su, H., Qian, K., Wofford, S., Zhao, X., Ivanov, I.* & Zheng Y.G. Diamidine compounds as selective inhibitors of protein arginine methyltransferase 1. Journal of Medicinal Chemistry (2014) 57, 2611–2622, doi:10.1021/jm401884z

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• Xu, X., Guardiani, C., Yan, C. & Ivanov, I.* Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1. Nucleic Acids Research (2013) 41, 10020-10031, doi:10.1093/nar/gkt810

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• Wang, L., Xu, X., Kumar, R., Maiti, B., Liu, C. T., Ivanov, I.*, Lee, T.-H. & Benkovic, S. J. Probing DNA clamps with single-molecule force spectroscopy. Nucleic Acids Research (2013) 41, 7804-7814, doi:10.1093/nar/gkt487

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• Brosey, C. A., Yan, C., Tsutakawa, S. E., Heller, W. T., Rambo, R. P., Tainer, J. A., Ivanov, I.* & Chazin, W. J. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Research (2013) 41, 2313-2327, doi:10.1093/nar/gks1332 (selected as a featured paper in the top 5% of NAR submissions)

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• Tsutakawa, S. E., Shin, D. S., Mol, C. D., Izumi, T., Arvai, A. S., Mantha, A. K., Szczesny, B., Ivanov, I. N., Hosfield, D. J., Maiti, B., Pique, M. E., Frankel, K. A., Hitomi, K., Cunningham, R. P., Mitra, S. & Tainer, J. A.  Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. Journal of Biological Chemistry (2013) 288, 8445-8455, doi:10.1074/jbc.M112.422774

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• Ivanov I.* Enzyme cofactors: Double-edged sword for catalysis. Nature Chemistry (2013) 5, 6-7, doi:10.1038/nchem.1529

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• Querol-Audi, J., Yan, C., Xu, X., Tsutakawa, S. E., Tsai, M.S., Tainer, J. A., Cooper, P. K., Nogales, E. & Ivanov, I.*  Repair complexes of FEN1, DNA and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proceedings of the National Academy of Sciences USA (2012) 109, 8528-8533, doi:10.1073/pnas.1121116109

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• Tsutakawa, S. E., Van Wynsberghe, A. W., Freudenthal, B. D., Weinacht, C. P., Gakhar, L., Washington, M. T., Zhuang, Z., Tainer, J. A. & Ivanov, I.* Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently-bound ubiquitin on PCNA. Proceedings of the National Academy of Sciences USA (2011) 108, 17672-17677, doi:10.1073/pnas.1110480108 (Faculty of 1000 recommended Factor 8.0; highlighted by the Oak Ridge Leadership Computing Facility)

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• Cheng, X. & Ivanov, I. Molecular dynamics. Methods in Molecular Biology (Clifton, N.J.) (2012) 929, 243-285. (Springer Protocols Series; ISBN 978-1-62703-049-6)

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• Feng, Y., Wang, J., Asher, S., Hoang, L., Guardiani, C., Ivanov, I.* & Zheng, Y. G. Histone H4 acetylation differentially modulates arginine methylation by an in Cis mechanism. Journal of Biological Chemistry (2011) 286, 20323-20334, doi:10.1074/jbc.M110.207258

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• Fritsch, S., Ivanov, I., Wang, H. & Cheng, X. Ion selectivity mechanism in a bacterial pentameric ligand gated ion channel. Biophysical Journal (2011) 100, 390-398, doi:10.1016/j.bpj.2010.11.077

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• Sander, T., Frolund, B., Bruun, A. T., Ivanov, I., McCammon, J. A. & Balle, T.  New insights into the GABA(a) receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data. Proteins: Structure Function and Bioinformatics (2011) 79, 1458-1477, doi:10.1002/prot.22975

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• Tainer, J. A., McCammon, J. A. & Ivanov, I.*  Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading. Journal of the American Chemical Society (2010) 132, 7372-7378, doi:10.1021/ja100365x (highlighted by the National Center for Computational Sciences)

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• Cheng, X., Ivanov, I., Wang, H., Sine, S. M. & McCammon, J. A. Molecular dynamics simulations of ELIC – a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophysical Journal (2009) 96, 4502-4513, doi:10.1016/j.bpj.2009.03.018

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• Amaro, R. E., Cheng, X., Ivanov, I., Xu, D. & McCammon, J. A.  Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via Generalized Born molecular dynamics and end-point free energy calculations. Journal of the American Chemical Society (2009) 131, 4702-4709, doi:10.1021/ja8085643

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• Som, A., Vemparala, S., Ivanov, I. & Tew, G. N. Synthetic mimics of antimicrobial peptides. Biopolymers (2008) 90, 83-93, doi:10.1002/bip.20970

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•  Gorfe, A. A., Chang, C. E. A., Ivanov, I. & McCammon, J. A. Dynamics of the acetylcholinesterase tetramer. Biophysical Journal (2008) 94, 1144-1154, doi:10.1529/biophysj.107.117879

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• Ivanov, I.*, Cheng, X., Sine, S. M. & McCammon, J. A.  Barriers to ion translocation in cationic and anionic receptors from the cys-loop family. Journal of the American Chemical Society (2007) 129, 8217-8224, doi:10.1021/ja070778l

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• Cheng, X., Ivanov, I.*, Wang, H., Sine, S. M. & McCammon, J. A.  Nanosecond time scale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophysical Journal (2007) 93, 2622-2634, doi:10.1529/biophysj.107.109843

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• Ivanov, I.*, Tainer, J. A. & McCammon, J. A. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme Endonuclease IV. Proceedings of the National Academy of Sciences USA (2007) 104, 1465-1470, doi:10.1073/pnas.0603468104

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• Ivanov, I.*, Chapados, B. R., McCammon, J. A. & Tainer, J. A. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Research (2006) 34, 6023-6033, doi:10.1093/nar/gkl744

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• Ivanov, I.*, Vemparala, S., Pophristic, V., Kuroda, K., DeGrado, W. F., McCammon, J. A. & Klein, M. L. Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces. Journal of the American Chemical Society (2006) 128, 1778-1779, doi:10.1021/ja0564665

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• Vemparala, S., Ivanov, I., Pophristic, V., Spiegel, K. & Klein, M. L. Ab initio calculations of intra bond parameters for a class of arylamide polymers. Journal of Computational Chemistry (2006) 27, 693-700, doi:10.1002/jcc.20382

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• Pophristic, V., Vemparala, S., Ivanov, I., Liu, Z. W., Klein, M. L. & DeGrado, W. F. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics and classical molecular dynamics study. Journal of Physical Chemistry B (2006) 110, 3517-3526, doi:10.1021/jp054306

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• Ivanov, I.*, Chen, B., Raugei, S. & Klein, M. L. Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation. Journal of Physical Chemistry B (2006) 110, 6365-6371, doi:10.1021/jp056750i

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• Choi, S., Clements, D. J., Pophristic, V., Ivanov, I., Vemparala, S., Bennett, J. S., Klein, M. L., Winkler, J. D. & DeGrado, W. E. The design and evaluation of heparin-binding foldamers. Angewandte Chemie-International Edition (2005) 44, 6685-6689, doi:10.1002/anie.200501279 (featured on the cover of Angewandte Chemie)

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• Ivanov, I.* & Klein, M. L. Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics methods. Journal of the American Chemical Society (2005) 127, 4010-4020, doi:10.1021/ja043693i

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• Ivanov, I. Terascale ab initio molecular dynamics simulations of proton transfer and dissociation processes in chemical and biological systems. (2004) ProQuest AAI3152059

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• Nielsen, S. O., Lopez, C. F., Ivanov, I., Moore, P. B., Shelley, J. C. & Klein, M. L. Transmembrane peptide induced lipid sorting and mechanism of L- alpha to inverted phase transition using coarse grain molecular dynamics. Biophysical Journal (2004) 87, 2107-2115, doi:10.1529/biophysj.104.040311

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• Chen, B., Ivanov, I., Klein, M. L. & Parrinello, M. Hydrogen bonding in water.  Physical Review Letters (2003) 91, doi:10.1103/PhysRevLett.91.215503 (cited over 250 times)

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• Ivanov, I.* & Klein, M. L. First principles computational study of the active site of arginase. Proteins: Structure Function and Genetics (2004) 54, 1-7, doi:10.1002/prot.10572

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• Min, G., Savin, D., Gu, Z., Patterson, G. D., Kim, S. H., Ramsay, D. J., Fishman, D., Ivanov, I., Sheina, E., Slaby, E. & Oliver, J. Solution characterization of monodisperse atactic polystyrenes by static and dynamic light scattering. International Journal of Polymer Analysis and Characterization (2003) 8, 187-207, doi:10.1080/10236660304875

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• Ivanov, I.* & Klein, M. L. Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics.  Journal of the American Chemical Society 2002 124, 13380-13381, doi:10.1021/ja027972m

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• Chen, B., Ivanov, I., Park, J. M., Parrinello, M. & Klein, M. L.   Solvation structure and mobility mechanism of OH-: A Car- Parrinello molecular dynamics investigation of alkaline solution. Journal of Physical Chemistry B  2002 106, 12006-12016, doi:10.1021/jp026504w

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• Chen, B., Park, J. M., Ivanov, I., Tabacchi, G., Klein, M. L. & Parrinello, M.  First-principles study of aqueous hydroxide solutions. Journal of the American Chemical Society 2002 124, 8534-8535, doi:10.1021/ja020350g

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• Ivanov, I., Gherman, B. F. & Yaron, D. Comparison of the INDO band structures of polyacetylene, polythiophene, polyfuran, and polypyrrole. Synthetic Metals 2001 116, 111-114, doi:10.1016/s0379-6779(00)00526-9

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