*Yesselman JD, *Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R, “RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix”, in preparation (Link | Paper| Preprint)
 Yesselman JD, Eiler D, Carlson ED, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Jewett MC, Kieft JS, Das R "Computational Design of Asymmetric Three-dimensional RNA Structures and Machines”, in revisions, Nature Nanotechnology (Link | Paper| Preprint)
 *Denny SK, *Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ, “High-throughput, quantitative
characterization of RNA tertiary structure elements”, Accepted, Cell (Link | Paper)
 *Yesselman JD, *Tian S, Lui X, Shi L, Li JB, Das R, "Updates to the RNA Mapping Database (RMDB), Version 2", Nucleic Acids Research (Link | Paper)
 Cheng CY*, Kladwang W*, Yesselman JD, Das R “Serendipitous high-resolution RNA structural information overlooked in dimethyl sulfate mapping experiments”, Proceedings of the National Academy of Sciences. (Link | Paper)
 Wang Y, Yesselman JD, Zhang, Q, Kang M, Feigon J, (2016) "Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human." Proceedings of the National Academy of Sciences. (Link | Paper)
Structural Comparison Between Medaka and Human Telemerase Pseudoknot
Comparison of minimal mdPK and hPK (PDB ID code 2K95) structures. Secondary structure elements are P2b (red), P3 (blue), J2a/3 (green), and J2b/3 (gold).
Model of active state transition in Tetrahymena ribozyme
Models for active site interactions within (E•S•G)O and (E•S•G)C.. The black arrows highlight changes in the positions of active site residues in going from (E•S•G)C to (E•S•G)O.
FARFAR RNA 3D Prediction Accuracy
A) GCAA tetraloop (1ZIH), RNA Denovo lowest energy models displays a high level of convergence. B) Pseudoknot (1L2X), less converged then tetraloop but also larger, still within 3Å heavy-atom rmsd for top model. C) 4x4 internal loop solved by NMR at PDB ID 2L8F, converges despite presenting 4 non-canonical base pairs.
RNA-Redesign Server Output
RP domain IV RNA (PDB ID: 1LNT) contains highly conserved AC base pairs that RNA-Redesign mutates to stabilize the RNA
Schematic and Runtime of the Primerize Algorithm
Schematic of the Primerize algorithm. Tm (STEP 1) and misprime matrices (STEP 2) are pre-calculated for the dynamic programming assembly.
Survey of C---OH Hydrogen Bonds in Proteins
Depiction of angles and distances measured. B: Methyl hydrogen donor to acceptor distances in which the acceptor is oxygen (solid line) or carbon (dashed line). Dashed-dot line is the difference of the latter curves. C: Elevation angles of methyl CH···O hydrogen bonds. D: Methyl CH···X angles in which X is oxygen (solid line) or carbon (dashed line).
Six Classes of AdoMet-dependent Methyltransferases
The hydrogen-bond donor and methyl C···O interaction distances are labeled in each enzyme.
Chemical Classes Requiring Additional Refinement
Average unsigned errors of hydration free energies for specific chemical classes for (top panel) CGENFF molecules and (bottom panel) non-CGENFF compounds.
Quality of the Minimized MATCH-Typed Molecules
PubChem drug-like molecules that were successfully processed using the CGENFF libraries within MATCH to generate their respective topology and parameter files. RMSD was computed by comparing conformations found in the PubChem database to the ones after minimization.
Locations of ionizable residues in Δ+PHS
Δ+PHS staphylococcal nuclease is shown here with all ionizing residues highlighted. Glutamic acid is cyan, and aspartic acid is orange. (From: Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics
Optimized active site with bound AdoMet
Truncated AdoMet and the protein are depicted with green and gray carbon atoms, respectively. Residues labeled in red designate CH O acceptors. H O distances from methyl protons to nearest oxygen atom for optimized and broken geometry are shown in magenta and cyan, respectively.