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 …
AmberTools
AmberTools | Journal of Chemical Information and Modeling ACS ACS Publications C&EN CAS
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Pathways to a shiny future: Building the foundation for computational physical chemistry and biophysics in 2050
In the last quarter-century, the field of molecular dynamics (MD) has undergone a
remarkable transformation, propelled by substantial enhancements in software, hardware …
remarkable transformation, propelled by substantial enhancements in software, hardware …
[HTML][HTML] Intrinsic disorder in the dynamic evolution of structure, stability, and flexibility of potyviral VLP assemblies: A computational study
LF Pacios, F Sánchez, F Ponz - International Journal of Biological …, 2024 - Elsevier
Abstract An all-atom Molecular Dynamics (MD) study was applied to three viral
nanoparticles (VLPs) of Turnip mosaic virus (TuMV), a potyvirus: the particles genetically …
nanoparticles (VLPs) of Turnip mosaic virus (TuMV), a potyvirus: the particles genetically …
Advancing one health vaccination: In silico design and evaluation of a multi-epitope subunit vaccine against Nipah virus for cross-species immunization using …
The resurgence of the Nipah virus (NiV) in 2023 has raised concerns for another potentially
severe pandemic, given its history of high mortality from previous outbreaks. Unfortunately …
severe pandemic, given its history of high mortality from previous outbreaks. Unfortunately …
Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields
M Domanska, P Setny - The Journal of Physical Chemistry B, 2024 - ACS Publications
Curvature emerges as a fundamental membrane characteristic crucial for diverse biological
processes, including vesicle formation, cell signaling, and membrane trafficking …
processes, including vesicle formation, cell signaling, and membrane trafficking …
A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the …
Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental
techniques due to their large-scale conformational fluctuations and transient structural …
techniques due to their large-scale conformational fluctuations and transient structural …
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
D Farré-Gil, JP Arcon, CA Laughton… - Nucleic Acids …, 2024 - academic.oup.com
We present CGeNArate, a new model for molecular dynamics simulations of very long
segments of B-DNA in the context of biotechnological or chromatin studies. The developed …
segments of B-DNA in the context of biotechnological or chromatin studies. The developed …
Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling …
Under physiological conditions, proteins continuously undergo structural fluctuations on
different timescales. Some conformations are only sparsely populated, but still play a key …
different timescales. Some conformations are only sparsely populated, but still play a key …
Creating coarse-grained systems with COBY: towards higher accuracy in membrane complexity
Current trends in molecular modelling are geared towards increasingly realistic
representations of the modelled systems. This is reflected in larger, more complex systems …
representations of the modelled systems. This is reflected in larger, more complex systems …