One-Bead Coarse-Grained Model for RNA 3D Structure with Non-Canonical Interactions
نویسندگان
چکیده
منابع مشابه
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grain...
متن کاملCoarse-grained model for predicting RNA folding thermodynamics.
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond, and electrostatic interactions as fundamental components in describing the stability of RNA structures. The stacking interactions are parametrized using a set of nucleotide-specific parameters, which were calibrated against the thermodyn...
متن کاملProtein secondary-structure description with a coarse-grained model.
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using ...
متن کاملProtein secondary structure analysis with a coarse-grained model
The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the Cα-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and describe the folding of the protein backbone by a succession of screw motions linking the Frenet frames at consecutive Cα-positions. Using the ASTRAL subset of the SCOPe data...
متن کاملSoft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.
Living cells contain diverse biopolymers, creating a heterogeneous crowding environment, the impact of which on RNA folding is poorly understood. Here, we have used single-molecule fluorescence resonance energy transfer to monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene glycol and yeast cell extract as crowding agents. As expected, po...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2019
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2018.11.1921