[HTML][HTML] Comparing the intrinsic dynamics of multiple protein structures using elastic network models
Abstract Background Elastic network models (ENMs) are based on the simple idea that a
protein can be described as a set of particles connected by springs, which can then be used …
protein can be described as a set of particles connected by springs, which can then be used …
Revisiting the Ramachandran plot based on statistical analysis of static and dynamic characteristics of protein structures
SW Park, BH Lee, SH Song, MK Kim - Journal of Structural Biology, 2023 - Elsevier
Ramachandran plots, which describe protein structures by plotting the dihedral angle pairs
of the backbone on a two-dimensional plane, have played an important role in structural …
of the backbone on a two-dimensional plane, have played an important role in structural …
Elastic Network Model: A Coarse-Grained Approach to the Study of Biomolecular Dynamics
SW Park, BH Lee, MK Kim - Multiscale Science and Engineering, 2023 - Springer
Over the past several decades, biomolecular dynamics has been extensively investigated
through both theoretical and experimental approaches to uncover the general relationship …
through both theoretical and experimental approaches to uncover the general relationship …
Comparisons of protein dynamics from experimental structure ensembles, molecular dynamics ensembles, and coarse-grained elastic network models
Predicting protein motions is important for bridging the gap between protein structure and
function. With growing numbers of structures of the same or closely related proteins …
function. With growing numbers of structures of the same or closely related proteins …
FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping
Coarse-grained models have become ubiquitous in biomolecular modeling tasks aimed at
studying slow dynamical processes such as protein folding and DNA hybridization. These …
studying slow dynamical processes such as protein folding and DNA hybridization. These …
Bridging between nma and elastic network models: preserving all-atom accuracy in coarse-grained models
Dynamics can provide deep insights into the functional mechanisms of proteins and protein
complexes. For large protein complexes such as GroEL/GroES with more than 8,000 …
complexes. For large protein complexes such as GroEL/GroES with more than 8,000 …
Ternary and senary representations using DNA double-crossover tiles
The information capacity of DNA double-crossover (DX) tiles was successfully increased
beyond a binary representation to higher base representations. By controlling the length and …
beyond a binary representation to higher base representations. By controlling the length and …
Robust elastic network model: A general modeling for precise understanding of protein dynamics
In the study of protein dynamics relevant to functions, normal mode analysis based on
elastic network models (ENMs) has become popular. These models are usually validated by …
elastic network models (ENMs) has become popular. These models are usually validated by …
Effect of solvent on protein structure and dynamics
AB Majumdar, IJ Kim, H Na - Physical Biology, 2020 - iopscience.iop.org
Understanding how much solvents influence the structures and dynamics of proteins is
important to understand functional mechanisms of solvated proteins. We propose a solvated …
important to understand functional mechanisms of solvated proteins. We propose a solvated …
Vibrational characteristics of DNA nanostructures obtained through a mass-weighted chemical elastic network model
Using the programmable and self-assembly characteristics of DNA, various DNA
nanostructures have been designed and synthesized for specific applications, such as …
nanostructures have been designed and synthesized for specific applications, such as …