| scholarly article | Q13442814 |
| P356 | DOI | 10.1016/J.YMETH.2019.03.023 |
| P698 | PubMed publication ID | 30935976 |
| P2093 | author name string | Paul C Whitford | |
| Jeffrey K Noel | |||
| Mariana Levi | |||
| P2860 | cites work | Structures of the bacterial ribosome in classical and hybrid states of tRNA binding | Q24635922 |
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| Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis | Q27653327 | ||
| GTPase activation of elongation factor EF-Tu by the ribosome during decoding | Q27653858 | ||
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| Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites | Q27666149 | ||
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| Scalable molecular dynamics with NAMD | Q27860718 | ||
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| Dynamics of folded proteins | Q28287584 | ||
| Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding | Q28294869 | ||
| Connecting the kinetics and energy landscape of tRNA translocation on the ribosome | Q28488598 | ||
| How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome | Q28822195 | ||
| Funnels, pathways, and the energy landscape of protein folding: a synthesis | Q29617521 | ||
| A ratchet-like inter-subunit reorganization of the ribosome during translocation | Q29619258 | ||
| A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions | Q30010194 | ||
| An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields | Q30157501 | ||
| P versus Q: structural reaction coordinates capture protein folding on smooth landscapes | Q30159963 | ||
| Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse | Q30167659 | ||
| Prediction of folding mechanism for circular-permuted proteins | Q30167986 | ||
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| Simulating movement of tRNA into the ribosome during decoding | Q30476304 | ||
| Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations | Q30477971 | ||
| The role of L1 stalk-tRNA interaction in the ribosome elongation cycle | Q30497195 | ||
| Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins | Q41734718 | ||
| A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest | Q41831230 | ||
| Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome | Q41914975 | ||
| Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome | Q41942083 | ||
| The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function | Q41956507 | ||
| Single-molecule fluorescence measurements of ribosomal translocation dynamics. | Q42088781 | ||
| Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. | Q42552807 | ||
| eSBMTools 1.0: enhanced native structure-based modeling tools | Q42617522 | ||
| Distortion of tRNA upon near-cognate codon recognition on the ribosome | Q42650025 | ||
| The ribosome structure controls and directs mRNA entry, translocation and exit dynamics | Q42719319 | ||
| Selection of optimal variants of Gō-like models of proteins through studies of stretching | Q42771246 | ||
| Brownian dynamics study of the association between the 70S ribosome and elongation factor G. | Q42778409 | ||
| Intermediate states in the movement of transfer RNA in the ribosome | Q44026748 | ||
| Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation | Q44718743 | ||
| Kinetic determinants of high-fidelity tRNA discrimination on the ribosome | Q44753572 | ||
| Ensemble cryo-EM elucidates the mechanism of translation fidelity | Q45059803 | ||
| Capturing Transition States for tRNA Hybrid-State Formation in the Ribosome | Q45296574 | ||
| How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics. | Q45300947 | ||
| Challenges in describing ribosome dynamics | Q45301161 | ||
| Anisotropic Fluctuations in the Ribosome Determine tRNA Kinetics. | Q45304207 | ||
| Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes | Q45323966 | ||
| Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates | Q46100119 | ||
| The importance of explicit chain representation in protein folding models: An examination of ising‐like models | Q46213311 | ||
| Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates | Q46797018 | ||
| RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. | Q47235409 | ||
| Effect of finite size on cooperativity and rates of protein folding. | Q47354039 | ||
| Origin of the omnipotence of eukaryotic release factor 1. | Q47408878 | ||
| Global ribosome motions revealed with elastic network model | Q47609027 | ||
| The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains | Q47633882 | ||
| Quantifying the Relationship between Single-Molecule Probes and Subunit Rotation in the Ribosome | Q47771591 | ||
| Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules | Q47933120 | ||
| Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? | Q48605842 | ||
| Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. | Q50708482 | ||
| Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. | Q51501726 | ||
| The antibiotic viomycin traps the ribosome in an intermediate state of translocation. | Q51985371 | ||
| Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. | Q52053541 | ||
| Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. | Q54839487 | ||
| Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach | Q56688819 | ||
| The ribosome and the mechanism of protein synthesis | Q56813741 | ||
| Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor | Q57875030 | ||
| Development and Applications of Coarse-Grained Models for RNA | Q58008452 | ||
| Disorder guides domain rearrangement in elongation factor Tu | Q58429273 | ||
| E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form | Q58788156 | ||
| The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation | Q73751182 | ||
| Polymer principles of protein calorimetric two-state cooperativity | Q74015806 | ||
| Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L | Q78968479 | ||
| A multiscale coarse-graining method for biomolecular systems | Q79935025 | ||
| Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation | Q81254271 | ||
| Protein sliding along DNA: dynamics and structural characterization | Q82851590 | ||
| Coarse-grained model for predicting RNA folding thermodynamics | Q86487529 | ||
| Structure-based energetics of mRNA decoding on the ribosome | Q87349314 | ||
| Dissecting the Energetics of Subunit Rotation in the Ribosome | Q92191232 | ||
| Trajectories of the ribosome as a Brownian nanomachine | Q30608405 | ||
| tRNA dynamics on the ribosome during translation | Q30832302 | ||
| Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM. | Q31046682 | ||
| Rate and accuracy of bacterial protein synthesis revisited | Q33327464 | ||
| The ribosome's energy landscape: Recent insights from computation | Q33639675 | ||
| Dynamics of translation on the ribosome: molecular mechanics of translocation | Q33660978 | ||
| Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM | Q33700051 | ||
| Reaction coordinates and rates from transition paths | Q33784292 | ||
| Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways | Q33867466 | ||
| Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes | Q33900447 | ||
| Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms | Q33950262 | ||
| SMOG@ctbp: simplified deployment of structure-based models in GROMACS | Q33957517 | ||
| What recent ribosome structures have revealed about the mechanism of translation | Q34019810 | ||
| Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. | Q34049310 | ||
| Structure and dynamics of a processive Brownian motor: the translating ribosome | Q34104360 | ||
| Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome | Q34155882 | ||
| Molecular mechanics of 30S subunit head rotation | Q34218305 | ||
| Bridging the gap between ribosome structure and biochemistry by mechanistic computations. | Q34376199 | ||
| Following movement of domain IV of elongation factor G during ribosomal translocation. | Q34409109 | ||
| Contact order, transition state placement and the refolding rates of single domain proteins. | Q34464266 | ||
| Connecting thermal and mechanical protein (un)folding landscapes | Q34727575 | ||
| Capturing transition paths and transition states for conformational rearrangements in the ribosome | Q34727629 | ||
| Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction | Q34772955 | ||
| Molecular dynamics simulations of biomolecules | Q34799927 | ||
| Conformational changes of elongation factor G on the ribosome during tRNA translocation | Q34978694 | ||
| Movement of elongation factor G between compact and extended conformations. | Q34979440 | ||
| The transition state for formation of the peptide bond in the ribosome | Q35011818 | ||
| Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome | Q35049159 | ||
| Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy | Q35234492 | ||
| Frustration in protein-DNA binding influences conformational switching and target search kinetics | Q35518582 | ||
| Excited states of ribosome translocation revealed through integrative molecular modeling | Q35571390 | ||
| Exploring the balance between folding and functional dynamics in proteins and RNA. | Q35585422 | ||
| Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection | Q35657607 | ||
| Protein topology determines binding mechanism | Q35734060 | ||
| How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta | Q35752174 | ||
| Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA | Q35891587 | ||
| Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? | Q35917424 | ||
| SMOG 2: A Versatile Software Package for Generating Structure-Based Models | Q35952382 | ||
| The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer | Q36024318 | ||
| Identification of two distinct hybrid state intermediates on the ribosome | Q36462728 | ||
| Diffusive reaction dynamics on invariant free energy profiles | Q36893547 | ||
| The ribosome in focus: new structures bring new insights | Q36926293 | ||
| Irreversible chemical steps control intersubunit dynamics during translation | Q36926818 | ||
| Biomolecular dynamics: order-disorder transitions and energy landscapes | Q36962788 | ||
| Stabilizing effect of knots on proteins | Q37018726 | ||
| Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles | Q37100851 | ||
| Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin | Q37114735 | ||
| Following movement of the L1 stalk between three functional states in single ribosomes. | Q37115162 | ||
| Simulating movement of tRNA through the ribosome during hybrid-state formation | Q37117033 | ||
| Native contacts determine protein folding mechanisms in atomistic simulations | Q37276492 | ||
| Minimal models for proteins and RNA from folding to function | Q37361859 | ||
| Fidelity at the molecular level: lessons from protein synthesis | Q37400330 | ||
| Insights from coarse-grained Gō models for protein folding and dynamics | Q37462223 | ||
| Proofreading of the codon-anticodon interaction on ribosomes | Q37598537 | ||
| Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches | Q37686070 | ||
| Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models | Q37859764 | ||
| Perspective on the Martini model. | Q38109488 | ||
| What protein folding teaches us about biological function and molecular machines | Q38307521 | ||
| Using the folding landscapes of proteins to understand protein function | Q38712096 | ||
| Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods | Q38887696 | ||
| Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. | Q39763452 | ||
| On Reaction Coordinate Optimality | Q40296077 | ||
| Spontaneous intersubunit rotation in single ribosomes. | Q41208124 | ||
| OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. | Q41327186 | ||
| Kinetically competent intermediates in the translocation step of protein synthesis | Q41353918 | ||
| Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome | Q41453877 | ||
| Picosecond dynamics of tyrosine side chains in proteins | Q41482271 | ||
| Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy | Q41618424 | ||
| P304 | page(s) | 128-140 | |
| P577 | publication date | 2019-03-30 | |
| P1433 | published in | Methods | Q6823859 |
| P1476 | title | Studying ribosome dynamics with simplified models | |
| P478 | volume | 162-163 |
| Q101573932 | A steric gate controls P/E hybrid-state formation of tRNA on the ribosome |
| Q92960309 | Experimental and computational techniques for studying structural dynamics and function of RNA |
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