Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
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 …
SPICA force field for proteins and peptides
S Kawamoto, H Liu, Y Miyazaki, S Seo… - Journal of Chemical …, 2022 - ACS Publications
A coarse-grained (CG) model for peptides and proteins was developed as an extension of
the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was …
the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was …
Transferable and polarizable coarse grained model for proteins─ ProMPT
The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-
grained level, FG), to most biomolecular processes, remains limited because of the …
grained level, FG), to most biomolecular processes, remains limited because of the …
Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
The physics-based united-residue (UNRES) model of proteins (www. unres. pl) has been
designed to carry out large-scale simulations of protein folding. The force field has been …
designed to carry out large-scale simulations of protein folding. The force field has been …
Organizations of melittin peptides after spontaneous penetration into cell membranes
The antimicrobial peptide, melittin, is a potential next-generation antibiotic because melittin
can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage …
can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage …
[HTML][HTML] The N-terminal proline hinge motif controls the structure of bovine herpesvirus 1-encoded inhibitor of the transporter associated with antigen processing …
Due to unique features, proline residues may control protein structure and function. Here, we
investigated the role of 52 PPQ 54 residues, indicated by the recently established …
investigated the role of 52 PPQ 54 residues, indicated by the recently established …
pSPICA Force Field Extended for Proteins and Peptides
Y Miyazaki, W Shinoda - Journal of Chemical Information and …, 2023 - ACS Publications
Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to
investigate biological processes involving proteins and lipids. CG force fields (FFs) in these …
investigate biological processes involving proteins and lipids. CG force fields (FFs) in these …
Long-time dynamics of selected molecular-motor components using a physics-based coarse-grained approach
A Liwo, M Pyrka, C Czaplewski, X Peng, AJ Niemi - Biomolecules, 2023 - mdpi.com
Molecular motors are essential for the movement and transportation of macromolecules in
living organisms. Among them, rotatory motors are particularly efficient. In this study, we …
living organisms. Among them, rotatory motors are particularly efficient. In this study, we …
Residue-level contact reveals modular domain interactions of PICK1 are driven by both electrostatic and hydrophobic forces
AO Stevens, Y He - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
PICK1 is a multi-domain scaffolding protein that is uniquely comprised of both a PDZ domain
and a BAR domain. While previous experiments have shown that the PDZ domain and the …
and a BAR domain. While previous experiments have shown that the PDZ domain and the …