SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
نویسندگان
چکیده
منابع مشابه
Coarse-Grained Prediction of RNA Loop Structures
One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed "Vfold" model (a coarse-grained RNA folding model) provides an effective method to generate the complete ense...
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 کاملGPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly
Molecular dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. We recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In our present study, we analy...
متن کاملCapturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), b...
متن کاملPrediction of protein structure by simulating coarse-grained folding pathways: a preliminary report.
A set of software tools designed to study protein structure and kinetics has been developed. The core of these tools is a program called Folding Machine (FM) which is able to generate low resolution folding pathways using modest computational resources. The FM is based on a coarse-grained kinetic ab initio Monte-Carlo sampler that can optionally use information extracted from secondary structur...
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: Nucleic Acids Research
سال: 2015
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkv1479