Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27026
Abstract: We report major algorithmic improvements of the UNRES package for physics‐based coarse‐grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to… read more here.
Keywords: grained simulations; parallel implementation; optimization parallel; implementation unres ... See more keywords
Direct determination of forces between charged nanogels through coarse-grained simulations.
Sign Up to like & getrecommendations! Published in 2018 at "Physical Review E"
DOI: 10.1103/physreve.97.042608
Abstract: In this work, electrostatic forces between charged nanogels are explored through coarse-grained simulations. These simulations allow us to explicitly consider the complex topology of these nanoparticles and provide reliable force values to examine highly charged… read more here.
Keywords: forces charged; charge; direct determination; coarse grained ... See more keywords
Coarse-grained simulations of lysozyme-silica-nanoparticle corona.
Sign Up to like & getrecommendations! Published in 2023 at "Biointerphases"
DOI: 10.1116/6.0002736
Abstract: Protein coronas, formed by proteins and nanomaterials, have various applications in the biomedical field. Here, large-scale simulations of protein coronas have been carried out by an efficient mesoscopic coarse-grained method with the BMW-MARTINI force field.… read more here.
Keywords: grained simulations; protein coronas; coarse; simulations lysozyme ... See more keywords
Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.826505
Abstract: Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction… read more here.
Keywords: single molecule; guanidine riboswitch; grained simulations; riboswitch ... See more keywords