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Ivaylo N. Ivanov, Ph.D. - Publications

Affiliations: 
2004 University of Pennsylvania, Philadelphia, PA, United States 
Area:
computer simulation of condensed molecular systems
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tsutakawa SE, Tsai CL, Yan C, Bralić A, Chazin WJ, Hamdan SM, Schärer OD, Ivanov I, Tainer JA. Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. Dna Repair. 96: 102972. PMID 33007515 DOI: 10.1016/J.Dnarep.2020.102972  0.329
2020 Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, 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 of the United States of America. PMID 32669428 DOI: 10.1073/Pnas.2006231117  0.31
2020 Dodd T, Yan C, Ivanov I. Simulation-based methods for model building and refinement in cryo-electron microscopy. Journal of Chemical Information and Modeling. PMID 32202798 DOI: 10.1021/Acs.Jcim.0C00087  0.32
2019 Perumal SK, Xu X, Yan C, Ivanov I, Benkovic SJ. Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps. Journal of Molecular Biology. PMID 31051173 DOI: 10.1016/J.Jmb.2019.04.035  0.353
2019 Carter EK, Laughlin-Toth S, Dodd T, Wilson WD, Ivanov I. Small molecule binders recognize DNA microstructural variations via an induced fit mechanism. Physical Chemistry Chemical Physics : Pccp. PMID 30629058 DOI: 10.1039/C8Cp05537H  0.4
2019 Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural & Molecular Biology. 26: 397-406. DOI: 10.2210/Pdb6O9M/Pdb  0.36
2019 Dodd TW, Ivanov I. Molecular Dynamics Simulations Reveal Multiple Roles of Polymerase Thumb Domain During Primer Strand Translocation in DNA Polymerase III Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.459  0.339
2018 Dodd T, Yan C, Kossmann BR, Martin K, Ivanov I. Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG. Proceedings of the National Academy of Sciences of the United States of America. PMID 29784784 DOI: 10.1073/Pnas.1803323115  0.337
2017 Zhang J, Qian K, Yan C, He M, Jassim BA, Ivanov I, Zheng YG. Discovery of Decamidine as a New and Potent PRMT1 Inhibitor. Medchemcomm. 8: 440-444. PMID 28649316 DOI: 10.1039/C6Md00573J  0.305
2017 Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. Elife. 6. PMID 28230529 DOI: 10.7554/Elife.21884  0.319
2017 Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Research. 45: 1297-1306. PMID 28180310 DOI: 10.1093/Nar/Gkw1232  0.362
2016 Kossmann BR, 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 & Medicinal Chemistry Letters. PMID 27262595 DOI: 10.1016/J.Bmcl.2016.05.065  0.359
2016 Turaga RC, Yin L, Yang JJ, Lee H, Ivanov I, Yan C, Yang H, Grossniklaus HE, Wang S, Ma C, Sun L, Liu ZR. Rational design of a protein that binds integrin αvβ3 outside the ligand binding site. Nature Communications. 7: 11675. PMID 27241473 DOI: 10.1038/Ncomms11675  0.331
2016 He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature. 533: 359-65. PMID 27193682 DOI: 10.1107/S0108767317097483  0.311
2016 Xu X, Yan C, Kossmann BR, Ivanov I. Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing. The Journal of Physical Chemistry. B. PMID 27109703 DOI: 10.1021/Acs.Jpcb.6B02082  0.381
2016 Musille PM, Kossmann BR, Kohn JA, Ivanov I, Ortlund EA. Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity. The Journal of Biological Chemistry. 291: 1411-26. PMID 26553876 DOI: 10.1074/Jbc.M115.662874  0.352
2015 Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA. Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Proceedings of the National Academy of Sciences of the United States of America. PMID 26715749 DOI: 10.1073/Pnas.1518960113  0.359
2015 Xu X, Yan C, Wohlhueter R, Ivanov I. Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. Computational and Structural Biotechnology Journal. 13: 492-503. PMID 26557958 DOI: 10.1016/J.Csbj.2015.08.005  0.312
2015 Tsutakawa SE, Yan C, Xu X, Zhuang Z, Todd Washington M, Tainer JA, Ivanov I. 112 Structurally distinct ubiquitin- and SUMO-modified PCNA: implications for their distinct roles in the DNA damage response. Journal of Biomolecular Structure & Dynamics. 33: 70-1. PMID 26103323 DOI: 10.1080/07391102.2015.1032745  0.334
2015 Brosey CA, Soss SE, Brooks S, Yan C, Ivanov I, Dorai K, Chazin WJ. Functional dynamics in replication protein a DNA binding and protein recruitment domains. Structure (London, England : 1993). 23: 1028-38. PMID 26004442 DOI: 10.1016/J.Str.2015.04.008  0.357
2015 Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response. Structure (London, England : 1993). 23: 724-33. PMID 25773143 DOI: 10.1016/J.Str.2015.02.008  0.334
2014 Tsutakawa S, Yan C, Xu X, Freudenthal B, Weinacht C, Zhuang Z, Washington T, Ivanov I. Structurally Distinct Complexes of Ubiquitin and Sumo-Modified PCNA Lead to Distinct DNA Damage Response Pathways Biophysical Journal. 106: 691a. DOI: 10.1016/J.Bpj.2013.11.3823  0.312
2014 Tsutakawa S, Arvai A, Sarker A, Querol-Audi J, Finger D, Nogales E, Ivanov I, Cooper P, Grasby J, Tainer J. Defining the Superfamily Conserved Mechanism for Flap Endonucleases FEN1 and XPG Specificity for 5' Flap DNA and DNA Bubbles, Respectively, by Hybrids Methods of Crystallography, SAXS, EM, and Computation Biophysical Journal. 106: 230a. DOI: 10.1016/J.Bpj.2013.11.1343  0.347
2013 Xu X, Guardiani C, Yan C, Ivanov IN. Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1 Nucleic Acids Research. 41: 10020-10031. PMID 24038358 DOI: 10.1093/Nar/Gkt810  0.318
2013 Wang L, Xu X, Kumar R, Maiti B, Liu CT, Ivanov I, Lee TH, Benkovic SJ. Probing DNA clamps with single-molecule force spectroscopy. Nucleic Acids Research. 41: 7804-14. PMID 23783571 DOI: 10.1093/Nar/Gkt487  0.362
2013 Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, et al. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. The Journal of Biological Chemistry. 288: 8445-55. PMID 23355472 DOI: 10.1074/Jbc.M112.422774  0.304
2013 Brosey CA, Yan C, Tsutakawa SE, Heller WT, Rambo RP, Tainer JA, Ivanov I, Chazin WJ. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Research. 41: 2313-27. PMID 23303776 DOI: 10.1093/Nar/Gks1332  0.368
2012 Querol-Audí J, Yan C, Xu X, Tsutakawa SE, Tsai MS, Tainer JA, Cooper PK, Nogales E, Ivanov I. Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proceedings of the National Academy of Sciences of the United States of America. 109: 8528-33. PMID 22586102 DOI: 10.1073/Pnas.1121116109  0.323
2011 Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, 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 of the United States of America. 108: 17672-7. PMID 22006297 DOI: 10.1073/Pnas.1110480108  0.334
2011 Sander T, Frølund B, Bruun AT, Ivanov I, Mccammon JA, 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. 79: 1458-1477. PMID 21365676 DOI: 10.1002/Prot.22975  0.318
2010 Tainer JA, McCammon JA, Ivanov I. 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. 132: 7372-7378. PMID 20455582 DOI: 10.1021/Ja100365X  0.326
2010 Ivanov I, Van Wynsberghe A, Tainer JA, McCammon J. Multiscale Modeling of PCNA - Ubiquitin Interactions Biophysical Journal. 98: 387a. DOI: 10.1016/J.Bpj.2009.12.2087  0.35
2009 Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophysical Journal. 96: 4502-13. PMID 19486673 DOI: 10.1016/J.Bpj.2009.03.018  0.331
2009 Zhiryakova D, Ivanov I, Ilieva S, Guncheva M, Galunsky B, Stambolieva N. Do N-terminal nucleophile hydrolases indeed have a single amino acid catalytic center? Febs Journal. 276: 2589-2598. PMID 19476497 DOI: 10.1111/J.1742-4658.2009.06987.X  0.303
2009 Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. 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. 131: 4702-9. PMID 19296611 DOI: 10.1021/Ja8085643  0.36
2008 Gorfe AA, Chang CE, Ivanov I, McCammon JA. Dynamics of the acetylcholinesterase tetramer. Biophysical Journal. 94: 1144-54. PMID 17921202 DOI: 10.1529/Biophysj.107.117879  0.375
2007 Ivanov I, Tainer JA, McCammon JA. Unraveling the three-metal-ion catalytic mechanism of the DNA repair endonuclease IV Proceedings of the National Academy of Sciences of the United States of America. 104: 1465-1470. PMID 17242363 DOI: 10.1073/Pnas.0603468104  0.358
2007 Ivanov I, Chen B, Raugei S, Klein ML. Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation. The Journal of Physical Chemistry. B. 110: 6365-71. PMID 16553455 DOI: 10.1021/Jp056750I  0.658
2006 Ivanov I, Chapados BR, McCammon JA, Tainer JA. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Research. 34: 6023-33. PMID 17071716 DOI: 10.1093/Nar/Gkl744  0.34
2006 Vemparala S, Ivanov I, Pophristic V, Spiegel K, Klein ML. Ab initio calculations of intramolecular parameters for a class of arylamide polymers. Journal of Computational Chemistry. 27: 693-700. PMID 16634095 DOI: 10.1002/Jcc.20382  0.691
2006 Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML, DeGrado WF. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study. The Journal of Physical Chemistry. B. 110: 3517-26. PMID 16494407 DOI: 10.1021/Jp054306+  0.71
2006 Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. Journal of the American Chemical Society. 128: 1778-9. PMID 16464062 DOI: 10.1021/Ja0564665  0.705
2005 Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. The design and evaluation of heparin-binding foldamers. Angewandte Chemie (International Ed. in English). 44: 6685-9. PMID 16094685 DOI: 10.1002/Anie.200501279  0.691
2005 Ivanov I, Klein ML. Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics. Journal of the American Chemical Society. 127: 4010-20. PMID 15771538 DOI: 10.1021/Ja043693I  0.497
2005 Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. Cover Picture: The Design and Evaluation of Heparin-Binding Foldamers (Angew. Chem. Int. Ed. 41/2005) Angewandte Chemie International Edition. 44: 6599-6599. DOI: 10.1002/Anie.200590137  0.692
2005 Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. Titelbild: The Design and Evaluation of Heparin-Binding Foldamers (Angew. Chem. 41/2005) Angewandte Chemie. 117: 6757-6757. DOI: 10.1002/Ange.200590136  0.692
2004 Nielsen SO, Lopez CF, Ivanov I, Moore PB, Shelley JC, Klein ML. Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics. Biophysical Journal. 87: 2107-15. PMID 15454415 DOI: 10.1529/Biophysj.104.040311  0.602
2004 Guncheva M, Ivanov I, Galunsky B, Stambolieva N, Kaneti J. Kinetic studies and molecular modelling attribute a crucial role in the specificity and stereoselectivity of penicillin acylase to the pair ArgA145-ArgB263. Febs Journal. 271: 2272-2279. PMID 15153118 DOI: 10.1111/J.1432-1033.2004.04170.X  0.348
2004 Ivanov I, Klein ML. First principles computational study of the active site of arginase. Proteins. 54: 1-7. PMID 14705018 DOI: 10.1002/Prot.10572  0.457
2003 Chen B, Ivanov I, Klein ML, Parrinello M. Hydrogen bonding in water. Physical Review Letters. 91: 215503. PMID 14683314 DOI: 10.1103/Physrevlett.91.215503  0.426
2003 Ivanov I, Klein ML. Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics. Journal of the American Chemical Society. 124: 13380-1. PMID 12418879 DOI: 10.1021/Ja027972M  0.482
2002 Chen B, Park JM, Ivanov I, Tabacchi G, Klein ML, Parrinello M. First-principles study of aqueous hydroxide solutions. Journal of the American Chemical Society. 124: 8534-5. PMID 12121087 DOI: 10.1021/Ja020350G  0.438
2002 Chen B, Ivanov I, Park JM, Parrinello M, Klein ML. Solvation Structure and Mobility Mechanism of OH-:  A Car−Parrinello Molecular Dynamics Investigation of Alkaline Solutions The Journal of Physical Chemistry B. 106: 12006-12016. DOI: 10.1021/Jp026504W  0.468
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