| Reparameterization of RNA χ torsion parameters for the AMBER force field and comparison to NMR spectra for cytidine and uridine I Yildirim, HA Stern, SD Kennedy, JD Tubbs, DH Turner Journal of chemical theory and computation 6 (5), 1520-1531, 2010 | 192 | 2010 |
| Allosteric transcriptional regulation via changes in the overall topology of the core promoter SJ Philips, M Canalizo-Hernandez, I Yildirim, GC Schatz, A Mondragón, ... Science 349 (6250), 877-881, 2015 | 140 | 2015 |
| Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer MG Costales, H Aikawa, Y Li, JL Childs-Disney, D Abegg, DG Hoch, ... Proceedings of the National Academy of Sciences 117 (5), 2406-2411, 2020 | 130 | 2020 |
| Stacking in RNA: NMR of four tetramers benchmark molecular dynamics DE Condon, SD Kennedy, BC Mort, R Kierzek, I Yildirim, DH Turner Journal of chemical theory and computation 11 (6), 2729-2742, 2015 | 114 | 2015 |
| Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra for single-stranded r (GACC) are improved by revised χ torsions I Yildirim, HA Stern, JD Tubbs, SD Kennedy, DH Turner The journal of physical chemistry B 115 (29), 9261-9270, 2011 | 108 | 2011 |
| Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules JL Childs-Disney, E Stepniak-Konieczna, T Tran, I Yildirim, HJ Park, ... Nature communications 4 (1), 2044, 2013 | 97 | 2013 |
| The hairpin form of r (G4C2) exp in c9ALS/FTD is repeat-associated non-ATG translated and a target for bioactive small molecules ZF Wang, A Ursu, JL Childs-Disney, R Guertler, WY Yang, V Bernat, ... Cell chemical biology 26 (2), 179-190. e12, 2019 | 95 | 2019 |
| Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters JL Chen, AL Dishler, SD Kennedy, I Yildirim, B Liu, DH Turner, MJ Serra Biochemistry 51 (16), 3508-3522, 2012 | 95 | 2012 |
| Methods to enable the design of bioactive small molecules targeting RNA MD Disney, I Yildirim, JL Childs-Disney Organic & biomolecular chemistry 12 (7), 1029-1039, 2014 | 84 | 2014 |
| Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs I Yildirim, SD Kennedy, HA Stern, JM Hart, R Kierzek, DH Turner Journal of chemical theory and computation 8 (1), 172-181, 2012 | 79 | 2012 |
| Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity JL Childs-Disney, I Yildirim, HJ Park, JR Lohman, L Guan, T Tran, ... ACS chemical biology 9 (2), 538-550, 2014 | 68 | 2014 |
| 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 … I Yildirim, E Kierzek, R Kierzek, GC Schatz The journal of physical chemistry B 118 (49), 14177-14187, 2014 | 63 | 2014 |
| A Dynamic Structural Model of Expanded RNA CAG Repeats: A Refined X-ray Structure and Computational Investigations Using Molecular Dynamics and Umbrella Sampling Simulations I Yildirim, HJ Park, MD Disney, GC Schatz Journal of the American Chemical Society, 2013 | 63 | 2013 |
| An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5′-UAA/5′-GAN internal loops studied by molecular dynamics methods K Réblová, Z Strelcova, P Kulhánek, I Besseova, DH Mathews, ... Journal of chemical theory and computation 6 (3), 910-929, 2010 | 59 | 2010 |
| A general fragment-based approach to identify and optimize bioactive ligands targeting RNA BM Suresh, W Li, P Zhang, KW Wang, I Yildirim, CG Parker, MD Disney Proceedings of the National Academy of Sciences 117 (52), 33197-33203, 2020 | 54 | 2020 |
| Contributions of Stacking, Preorganization, and Hydrogen Bonding to the Thermodynamic Stability of Duplexes between RNA and 2′-O-Methyl RNA with Locked … E Kierzek, A Pasternak, K Pasternak, Z Gdaniec, I Yildirim, DH Turner, ... Biochemistry 48 (20), 4377-4387, 2009 | 54 | 2009 |
| RNA challenges for computational chemists I Yildirim, DH Turner Biochemistry 44 (40), 13225-13234, 2005 | 53 | 2005 |
| 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 … I Yildirim, HA Stern, J Sponer, N Spackova, DH Turner Journal of Chemical Theory and Computation 5 (8), 2088-2100, 2009 | 50 | 2009 |
| Zinc porphyrin: A fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer AA Ensign, I Jo, I Yildirim, TD Krauss, KL Bren Proceedings of the National Academy of Sciences 105 (31), 10779-10784, 2008 | 47 | 2008 |
| Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold–small molecule interactions HS Haniff, L Knerr, X Liu, G Crynen, J Boström, D Abegg, A Adibekian, ... Nature chemistry 12 (10), 952-961, 2020 | 44 | 2020 |
Matthew D. DisneyThe Scripps Research InstituteVerified email at scripps.edu
