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Ilyas Yildirim, Ph.D. - Publications

Affiliations: 
University of Rochester, Rochester, NY 
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40 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
2023 Taghavi A, Baisden JT, Childs-Disney JL, Yildirim I, Disney MD. Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies. Nucleic Acids Research. PMID 37216594 DOI: 10.1093/nar/gkad403  0.3
2022 Wang KW, Riveros I, DeLoye J, Yildirim I. Dynamic Docking of Small Molecules Targeting RNA CUG Repeats Causing Myotonic Dystrophy Type 1 (DM1). Biophysical Journal. PMID 36348626 DOI: 10.1016/j.bpj.2022.11.010  0.39
2022 Taghavi A, Riveros I, Wales DJ, Yildirim I. Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations. Journal of Chemical Theory and Computation. 18: 3637-3653. PMID 35652685 DOI: 10.1021/acs.jctc.2c00178  0.446
2022 Taghavi A, Yildirim I. Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders. Frontiers in Molecular Biosciences. 9: 830161. PMID 35480881 DOI: 10.3389/fmolb.2022.830161  0.47
2021 Ursu A, Baisden JT, Bush JA, Taghavi A, Choudhary S, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD. A Small Molecule Exploits Hidden Structural Features within the RNA Repeat Expansion That Causes c9ALS/FTD and Rescues Pathological Hallmarks. Acs Chemical Neuroscience. 12: 4076-4089. PMID 34677935 DOI: 10.1021/acschemneuro.1c00470  0.423
2021 Vezina-Dawod S, Angelbello AJ, Choudhary S, Wang KW, Yildirim I, Disney MD. Massively Parallel Optimization of the Linker Domain in Small Molecule Dimers Targeting a Toxic r(CUG) Repeat Expansion. Acs Medicinal Chemistry Letters. 12: 907-914. PMID 34141068 DOI: 10.1021/acsmedchemlett.1c00027  0.388
2020 Suresh BM, Li W, Zhang P, Wang KW, Yildirim I, Parker CG, Disney MD. A general fragment-based approach to identify and optimize bioactive ligands targeting RNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 33318191 DOI: 10.1073/pnas.2012217117  0.317
2020 Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD. Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD. Acs Chemical Biology. PMID 33196168 DOI: 10.1021/acschembio.0c00049  0.345
2020 Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD. A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. Cell Chemical Biology. PMID 33157036 DOI: 10.1016/j.chembiol.2020.10.007  0.405
2020 Haniff HS, Knerr L, Liu X, Crynen G, Boström J, Abegg D, Adibekian A, Lekah E, Wang KW, Cameron MD, Yildirim I, Lemurell M, Disney MD. Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold-small molecule interactions. Nature Chemistry. PMID 32839603 DOI: 10.1038/S41557-020-0514-4  0.427
2020 Benhamou R, Vezina-Dawod S, Choudhary S, Wang KW, Meyer SM, Yildirim I, Disney M. Macrocyclization of a ligand targeting a toxic RNA dramatically improves potency. Chembiochem : a European Journal of Chemical Biology. PMID 32649032 DOI: 10.1002/Cbic.202000445  0.471
2020 Costales MG, Aikawa H, Li Y, Childs-Disney JL, Abegg D, Hoch DG, Pradeep Velagapudi S, Nakai Y, Khan T, Wang KW, Yildirim I, Adibekian A, Wang ET, Disney MD. Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer. Proceedings of the National Academy of Sciences of the United States of America. PMID 31964809 DOI: 10.1073/Pnas.1914286117  0.436
2019 Yildirim I. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field. Methods in Molecular Biology (Clifton, N.J.). 2022: 55-74. PMID 31396899 DOI: 10.1007/978-1-4939-9608-7_3  0.501
2018 Wales DJ, Disney MD, Yildirim I. Computational Investigation of RNA A-Bulges Related to Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism. The Journal of Physical Chemistry. B. PMID 30517788 DOI: 10.1021/Acs.Jpcb.8B09139  0.48
2018 Wang ZF, Ursu A, Childs-Disney JL, Guertler R, Yang WY, Bernat V, Rzuczek SG, Fuerst R, Zhang YJ, Gendron TF, Yildirim I, Dwyer BG, Rice JE, Petrucelli L, Disney MD. The Hairpin Form of r(GC) in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules. Cell Chemical Biology. PMID 30503283 DOI: 10.1016/J.Chembiol.2018.10.018  0.42
2017 Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD. Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1. Biochemistry. PMID 28617590 DOI: 10.1021/Acs.Biochem.7B00252  0.506
2017 Wales DJ, Yildirim I. Improving Computational Predictions of Single-stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field. The Journal of Physical Chemistry. B. PMID 28319659 DOI: 10.1021/Acs.Jpcb.7B00819  0.508
2015 Yildirim I, Chakraborty D, Disney MD, Wales DJ, Schatz GC. Computational Investigation of RNA CUG Repeats Responsible for Myotonic Dystrophy 1. Journal of Chemical Theory and Computation. 11: 4943-4958. PMID 26500461 DOI: 10.1021/Acs.Jctc.5B00728  0.417
2015 Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragón A, O'Halloran TV. TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Science (New York, N.Y.). 349: 877-81. PMID 26293965 DOI: 10.1126/Science.Aaa9809  0.35
2015 Condon DE, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH. Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 2729-2742. PMID 26082675 DOI: 10.1021/Ct501025Q  0.45
2015 Park H, González ÀL, Yildirim I, Tran T, Lohman JR, Fang P, Guo M, Disney MD. Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10). Biochemistry. 54: 3851-9. PMID 26039897 DOI: 10.1021/Acs.Biochem.5B00551  0.501
2014 Yildirim I, Kierzek E, Kierzek R, Schatz GC. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results. The Journal of Physical Chemistry. B. 118: 14177-87. PMID 25268896 DOI: 10.1021/Jp506703G  0.497
2014 Yildirim I, Eryazici I, Nguyen ST, Schatz GC. Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities. The Journal of Physical Chemistry. B. 118: 2366-76. PMID 24494718 DOI: 10.1021/Jp501041M  0.306
2014 Condon DE, Yildirim I, Kennedy SD, Mort BC, Kierzek R, Turner DH. Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU). The Journal of Physical Chemistry. B. 118: 1216-28. PMID 24377321 DOI: 10.1021/Jp408909T  0.428
2014 Disney MD, Yildirim I, Childs-Disney JL. Methods to enable the design of bioactive small molecules targeting RNA. Organic & Biomolecular Chemistry. 12: 1029-39. PMID 24357181 DOI: 10.1039/C3Ob42023J  0.501
2014 Childs-Disney JL, Yildirim I, Park H, Lohman JR, Guan L, Tran T, Sarkar P, Schatz GC, Disney MD. Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity. Acs Chemical Biology. 9: 538-50. PMID 24341895 DOI: 10.1021/Cb4007387  0.455
2013 Childs-Disney JL, Stepniak-Konieczna E, Tran T, Yildirim I, Park H, Chen CZ, Hoskins J, Southall N, Marugan JJ, Patnaik S, Zheng W, Austin CP, Schatz GC, Sobczak K, Thornton CA, et al. Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules. Nature Communications. 4: 2044. PMID 23806903 DOI: 10.1038/Ncomms3044  0.372
2013 Yildirim I, Park H, Disney MD, Schatz GC. A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. Journal of the American Chemical Society. 135: 3528-38. PMID 23441937 DOI: 10.1021/Ja3108627  0.417
2013 Childs-Disney J, Yildirim I, Park H, Lohman J, Guan L, Tran T, Sarkar P, Schatz GC, Disney. Myotonic Dystrophy Type 2 RNA: Structural Studies and Designed Small Molecules that Modulate RNA Function Acs Chemical Biology. DOI: 10.2210/Pdb4K27/Pdb  0.488
2012 Chen JL, Dishler AL, Kennedy SD, Yildirim I, Liu B, Turner DH, Serra MJ. Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters. Biochemistry. 51: 3508-22. PMID 22490167 DOI: 10.1021/Bi3002709  0.486
2012 Eryazici I, Yildirim I, Schatz GC, Nguyen ST. Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: an experimental-computational study. Journal of the American Chemical Society. 134: 7450-8. PMID 22428783 DOI: 10.1021/Ja300322A  0.319
2012 Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH. Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs. Journal of Chemical Theory and Computation. 8: 172-181. PMID 22249447 DOI: 10.1021/Ct200557R  0.47
2011 Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions. The Journal of Physical Chemistry. B. 115: 9261-70. PMID 21721539 DOI: 10.1021/Jp2016006  0.463
2010 Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 6: 910-29. PMID 26613316 DOI: 10.1021/Ct900440T  0.459
2010 Réblová K, St?elcová Z, Kulhánek P, Beššeová I, Mathews DH, Nostrand KV, Yildirim I, Turner DH, Sponer J. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. Journal of Chemical Theory and Computation. 2010: 910-929. PMID 21132104  0.38
2010 Yildirim I, Stern HA, Kennedy SD, Tubbs JD, Turner DH. Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine. Journal of Chemical Theory and Computation. 6: 1520-1531. PMID 20463845 DOI: 10.1021/Ct900604A  0.398
2009 Yildirim I, Stern HA, Sponer J, Spackova N, Turner DH. Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs. Journal of Chemical Theory and Computation. 5: 2088-2100. PMID 20090924 DOI: 10.1021/Ct800540C  0.442
2009 Kierzek E, Pasternak A, Pasternak K, Gdaniec Z, Yildirim I, Turner DH, Kierzek R. Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids. Biochemistry. 48: 4377-87. PMID 19348504 DOI: 10.1021/Bi9002056  0.467
2007 Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD. Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs. The Journal of Physical Chemistry. B. 111: 6718-27. PMID 17411085 DOI: 10.1021/Jp068732M  0.451
2005 Yildirim I, Turner DH. RNA challenges for computational chemists. Biochemistry. 44: 13225-34. PMID 16201748 DOI: 10.1021/Bi051236O  0.47
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