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Protein dynamics

Jingjie Yeo's picture

Adsorption and Conformational Evolution of Alpha-Helical BSA Segments on Graphene: A Molecular Dynamics Study Molecular dynamics (MD) simulations are performed to investigate the adsorption mechanics and conformational dynamics of single and multiple bovine serum albumin (BSA) peptide segments on single-layer graphene through analysis of parameters such as the root-mean-square displacements, number of hydrogen bonds, helical content, inter- action energies, and motions of mass center of the peptides.

Review: Coarse-grained model for normal mode analysis of proteins

The preprint provides the summary and/or review of current state-of-art in coarse-grained modeling of protein structures for normal mode analysis. This review summarizes the quasiharmonic analysis, Go model, elastic network model, and recently suggested coarse-grained models for protein structures.


Model Reduction of Large Proteins for Normal Mode Studies

Recently, I reported the model reduction method for large proteins for understanding large protein dynamics based on low-frequency normal modes. This work was pubslihed at Journal of Computational Chemistry (click here).

Coarse-Graining of protein structures for the normal mode studies


Elastic model for proteins (polymers)

There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.

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