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 …
ClustENM: ENM-based sampling of essential conformational space at full atomic resolution
Accurate sampling of conformational space and, in particular, the transitions between
functional substates has been a challenge in molecular dynamic (MD) simulations of large …
functional substates has been a challenge in molecular dynamic (MD) simulations of large …
Novel RyR2 mutation (G3118R) is associated with autosomal recessive ventricular fibrillation and sudden death: clinical, functional, and computational analysis
Background The cardiac ryanodine receptor type 2 (RyR2) is a large homotetramer, located
in the sarcoplasmic reticulum (SR), which releases Ca2+ from the SR during systole. The …
in the sarcoplasmic reticulum (SR), which releases Ca2+ from the SR during systole. The …
Effect of dimerization on the dynamics of neurotransmitter: sodium symporters
Dimerization is a common feature among the members of the neurotransmitter: sodium
symporter (NSS) family of membrane proteins. Yet, the effect of dimerization on the …
symporter (NSS) family of membrane proteins. Yet, the effect of dimerization on the …
Normal mode-guided transition pathway generation in proteins
The biological function of proteins is closely related to its structural motion. For instance,
structurally misfolded proteins do not function properly. Although we are able to …
structurally misfolded proteins do not function properly. Although we are able to …
Frustration‐guided motion planning reveals conformational transitions in proteins
D Budday, R Fonseca, S Leyendecker… - Proteins: Structure …, 2017 - Wiley Online Library
Proteins exist as conformational ensembles, exchanging between substates to perform their
function. Advances in experimental techniques yield unprecedented access to structural …
function. Advances in experimental techniques yield unprecedented access to structural …
The energetics of subunit rotation in the ribosome
Protein synthesis in the cell is controlled by an elaborate sequence of conformational
rearrangements in the ribosome. The composition of a ribosome varies by species, though …
rearrangements in the ribosome. The composition of a ribosome varies by species, though …
A better prediction of conformational changes of proteins using minimally connected network models
Elastic network models have recently been used for studying low-frequency collective
motions of proteins. These models simplify the complexity that arises from normal mode …
motions of proteins. These models simplify the complexity that arises from normal mode …
Exploring conformational space with thermal fluctuations obtained by normal-mode analysis
Proteins in their native states can be represented as ensembles of conformers in dynamical
equilibrium. Thermal fluctuations are responsible for transitions between these conformers …
equilibrium. Thermal fluctuations are responsible for transitions between these conformers …