This site uses cookies. Note: This functionality works only for purchases done as a guest. SimRNA is a computational method for RNA folding simulations and 3D structure prediction. We outline the importance of classical secondary structure during all those levels of structure prediction.



(b) Time-evolved structure after 3.2 ps of dynamica...Figure 5: Structural model of F0F1-ATP synthase. RNAs adopt specific structures to perform their activities and these are critical to virtually all RNA-mediated processes. We summarize different levels of RNA structure prediction, from classical 2D structure to extended secondary structure and motif-based research toward 3D structure prediction of RNA. Acta Bioenerg.



Yi Xiao.



The leading hypothesis centers on radical pairs—...Figure 1: The principle of a radical-pair compass.



As virtually every method for simulations of molecular systems, it comprises three main functional elements: a representation of the molecules that are simulated, a scoring function (energy) and an algorithm that controls the moves of the molecular system. QUARK is a computer algorithm for ab initio protein structure prediction and protein peptide folding, which aims to construct the correct protein 3D model from amino acid sequence only. kS and kC are the rate constants of...Figure 7: Time dependence of a reacting radical pair and its reaction product. Jeffrey Skolnick, Bernhard C. Thiel, Christoph Flamm, Ivo L. Hofacker; RNA structure prediction: from 2D to 3D. The figure has been reproduced from Senior AE, Nadanaciva S, Weber J. We have recently introduced SimRNA, a method for RNA folding simulation and 3D structure prediction that uses a coarse-grained representation of five atoms per residue and a statistical potential methodology . We outline the importance of classical secondary structure during all those levels of structure prediction. Biophys. PDF + 7 Day HTML Access to this Article - Online Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation. Vienna RNA secondary structure prediction (University of Vienna, Austria). (a) Schematic representation of the reaction with definitions for the distances RAB, RAC, and RBC. Search for other works by this author on:

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Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.


Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation. 2002.

Jian Wang.

...Figure 1: Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to crowded medium and standard free energy of (a) association in solu...Figure 2: Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to confined volume element and standard free energy of (a) associatio...Figure 3: Dependence of the equilibrium constant for formation of a spherocylindrical dimer from two spherical monomers (R1 = 1) upon the volume fraction φ of hard-sphere crowders and dimer shape at c...Figure 4: Dependence of the equilibrium constant for binding of a spherical macromolecular ligand to an immobile surface site upon the volume fraction φ of hard-sphere crowders, with MWligand/MWcrowde...Figure 5: Effect of confinement in a spherical cavity on the free energy of two-state folding, calculated as a function of cavity radius according to the theory of Zhou & Dill (101), for proteins cont...AbstractI was born in Vienna and came to the United States as a refugee in October 1938.







PDF + 7 Day HTML Access to this Article - Online The gray disks represent the unpaired electrons, one on each radical, and the red arrows represent their spins.

(b) It...Figure 10: Schematic cross section through the retina showing the locations of the various cell types relative to the direction of the incoming light.


Insight into why the outcome of a radical-pair reaction can be significantly affected by extremely small magnetic interactions can be obtained from thi...Figure 3: Molecular orbitals and hyperfine interactions in flavin and tryptophan radicals.

We summarize different levels of RNA structure prediction, from classical 2D structure to extended secondary structure and motif-based research toward 3D structure prediction of RNA.




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