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Sosnick, Tobin R.
One or more keywords matched the following properties of Sosnick, Tobin R.
PropertyValue
keywords Simulations, Molecular Dynamics
overview My research program involves synergistic studies of protein folding and design, protein-RNA interactions, phosphorylation, signaling, and function with both experimental and computational components. The research is based on the premise that rigorous and innovative studies of basic processes have broad implications in many areas of biological research. My lab employs a range of experimental and computational methods including hydrogen exchange (HX), NMR, small-angle X-ray scattering (SAXS), rapid mixing methods, mass spectrometry, molecular dynamics and home-grown coarse-grain folding simulations and modeling. I am a very a strong believer in collaboration, having co-mentored over twenty students and post-doctoral fellows who produce over 60 papers in the last 20 years. I have a history of developing multi-approaches to bear on a problem. Since my Ph.D. in low temperature physics in 1989, I have entered many different areas, including delineating protein and RNA folding pathways and denatured states, de novo structure prediction, and the design of light-sensitive allosteric proteins.
One or more keywords matched the following items that are connected to Sosnick, Tobin R.
Item TypeName
Concept Computer Simulation
Concept Molecular Dynamics Simulation
Academic Article Dynamics of hydrogen bond desolvation in protein folding.
Academic Article Large-scale context in protein folding: villin headpiece.
Academic Article Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.
Academic Article Methods for the accurate estimation of confidence intervals on protein folding phi-values.
Academic Article RNA folding during transcription.
Academic Article Folding of a universal ribozyme: the ribonuclease P RNA.
Academic Article Quantifying the structural requirements of the folding transition state of protein A and other systems.
Academic Article Psi-constrained simulations of protein folding transition states: implications for calculating.
Academic Article Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.
Academic Article Small proteins fold through transition states with native-like topologies.
Academic Article New era of molecular structure and dynamics from solution scattering experiments.
Academic Article Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.
Academic Article De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.
Academic Article Modeling large regions in proteins: applications to loops, termini, and folding.
Academic Article The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).
Academic Article Modeling the hydration layer around proteins: HyPred.
Academic Article Early collapse is not an obligate step in protein folding.
Academic Article Differences in the folding transition state of ubiquitin indicated by phi and psi analyses.
Academic Article Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Academic Article The amino-terminal helix modulates light-activated conformational changes in AsLOV2.
Academic Article Simplified protein models: predicting folding pathways and structure using amino acid sequences.
Academic Article Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.
Academic Article Benchmarking all-atom simulations using hydrogen exchange.
Academic Article Ionic strength independence of charge distributions in solvation of biomolecules.
Academic Article A novel implicit solvent model for simulating the molecular dynamics of RNA.
Academic Article Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.
Academic Article Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.
Academic Article A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.
Academic Article Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
Academic Article Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
Academic Article On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.
Academic Article Molecular dynamics study of water channels in natural and synthetic amyloid-ß fibrils.
Academic Article Folding and misfolding of potassium channel monomers during assembly and tetramerization.
Academic Article Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation.
Concept Molecular Docking Simulation
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