| MATCH: An atom‐typing toolset for molecular mechanics force fields JD Yesselman, DJ Price, JL Knight, CL Brooks III Journal of Computational Chemistry, 2011 | 196 | 2011 |
| Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang, S Li, G Pintilie, ... Nature methods 17 (7), 699-707, 2020 | 170 | 2020 |
| RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers Z Miao, RW Adamiak, M Antczak, MJ Boniecki, J Bujnicki, SJ Chen, ... Rna 26 (8), 982-995, 2020 | 136 | 2020 |
| Conservation and functional importance of carbon–oxygen hydrogen bonding in AdoMet-dependent methyltransferases S Horowitz, LMA Dirk, JD Yesselman, JS Nimtz, U Adhikari, RA Mehl, ... Journal of the American Chemical Society 135 (41), 15536-15548, 2013 | 119 | 2013 |
| High-throughput investigation of diverse junction elements in RNA tertiary folding SK Denny, N Bisaria, JD Yesselman, R Das, D Herschlag, WJ Greenleaf Cell 174 (2), 377-390. e20, 2018 | 94 | 2018 |
| Computational design of three-dimensional RNA structure and function JD Yesselman, D Eiler, ED Carlson, MR Gotrik, AE d’Aquino, AN Ooms, ... Nature nanotechnology 14 (9), 866-873, 2019 | 84 | 2019 |
| Direct evidence for methyl group coordination by CH··· O hydrogen bonds in SET domain methyltransferases S Horowitz, JD Yesselman, HM Al-Hashimi, RC Trievel Journal of Biological Chemistry, 2011 | 76* | 2011 |
| Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction H Shi, A Rangadurai, H Abou Assi, R Roy, DA Case, D Herschlag, ... Nature communications 11 (1), 5531, 2020 | 69 | 2020 |
| RNA structure inference through chemical mapping after accidental or intentional mutations CY Cheng, W Kladwang, JD Yesselman, R Das Proceedings of the National Academy of Sciences 114 (37), 9876-9881, 2017 | 65 | 2017 |
| Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics EJ Arthur, JD Yesselman, CL Brooks III Proteins: Structure, Function, and Bioinformatics, 2011 | 55 | 2011 |
| Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures M Zafferani, C Haddad, L Luo, J Davila-Calderon, LY Chiu, CS Mugisha, ... Science advances 7 (48), eabl6096, 2021 | 52 | 2021 |
| Primerize: automated primer assembly for transcribing non-coding RNA domains S Tian, JD Yesselman, P Cordero, R Das Nucleic acids research 43 (W1), W522-W526, 2015 | 47 | 2015 |
| Frequent side chain methyl carbon‐oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures JD Yesselman, S Horowitz, CL Brooks III, RC Trievel Proteins: Structure, Function, and Bioinformatics 83 (3), 403-410, 2015 | 47 | 2015 |
| Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation JD Yesselman, SK Denny, N Bisaria, D Herschlag, WJ Greenleaf, R Das Proceedings of the National Academy of Sciences 116 (34), 16847-16855, 2019 | 41 | 2019 |
| Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes JL Knight, JD Yesselman, CL Brooks III Journal of computational chemistry 34 (11), 893-903, 2013 | 39 | 2013 |
| Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells R Van Damme, K Li, M Zhang, J Bai, WH Lee, JD Yesselman, Z Lu, ... Nature Communications 13 (1), 911, 2022 | 36 | 2022 |
| Updates to the RNA mapping database (RMDB), version 2 JD Yesselman, S Tian, X Liu, L Shi, JB Li, R Das Nucleic Acids Research 46 (D1), D375-D379, 2018 | 26 | 2018 |
| Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human Y Wang, JD Yesselman, Q Zhang, M Kang, J Feigon Proceedings of the National Academy of Sciences 113 (35), E5125-E5134, 2016 | 26 | 2016 |
| Modeling small noncanonical RNA motifs with the Rosetta FARFAR server JD Yesselman, R Das RNA Structure Determination: Methods and Protocols, 187-198, 2016 | 16 | 2016 |
| RNA-Redesign: a web server for fixed-backbone 3D design of RNA JD Yesselman, R Das Nucleic Acids Research 43 (W1), W498-W501, 2015 | 13 | 2015 |
