Related papers: Molecular dynamics simulations of chemically modif…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamental tool to characterize biomolecular dynamics and their…
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative…