RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
[HTML][HTML] Theory and practice of coarse-grained molecular dynamics of biologically important systems
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate
biomolecular systems at large time and size scales, compared to those accessible to all …
biomolecular systems at large time and size scales, compared to those accessible to all …
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale …
The general theory of the construction of scale-consistent energy terms in the coarse-
grained force fields presented in Paper I of this series has been applied to the revision of the …
grained force fields presented in Paper I of this series has been applied to the revision of the …
[HTML][HTML] Computational modeling of DNA 3D structures: From dynamics and mechanics to folding
DNA carries the genetic information required for the synthesis of RNA and proteins and
plays an important role in many processes of biological development. Understanding the …
plays an important role in many processes of biological development. Understanding the …
Insight into the initial stages of the folding process in onconase revealed by UNRES
The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …
biological function. This state is characterized by a large degree of structural heterogeneity …
[HTML][HTML] Modeling, simulations, and bioinformatics at the service of RNA structure
Although chemically close to DNA, RNA can adopt a wide range of structures from regular
helices to complex globular conformations, showing a complexity similar to that of proteins …
helices to complex globular conformations, showing a complexity similar to that of proteins …
Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA− Protein Complexes
D Chakraborty, B Mondal… - Journal of Chemical …, 2024 - ACS Publications
DNA–protein interactions are pervasive in a number of biophysical processes ranging from
transcription and gene expression to chromosome folding. To describe the structural and …
transcription and gene expression to chromosome folding. To describe the structural and …
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
In this chapter the scale-consistent approach to the derivation of coarse-grained force fields
developed in our laboratory is presented, in which the effective energy function originates …
developed in our laboratory is presented, in which the effective energy function originates …
[HTML][HTML] Ab initio predictions for 3D structure and stability of single-and double-stranded DNAs in ion solutions
ZC Mu, YL Tan, BG Zhang, J Liu… - PLOS Computational …, 2022 - journals.plos.org
The three-dimensional (3D) structure and stability of DNA are essential to
understand/control their biological functions and aid the development of novel materials. In …
understand/control their biological functions and aid the development of novel materials. In …
Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server
Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded
proteins, resulting in a lack of hydrophobic core (s) and a tendency to adopt rapidly …
proteins, resulting in a lack of hydrophobic core (s) and a tendency to adopt rapidly …