Local and long range potentials for heparin-protein systems for coarse-grained simulations.
Sign Up to like & getrecommendations! Published in 2019 at "Biopolymers"
DOI: 10.1002/bip.23269
Abstract: Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved… read more here.
Keywords: potentials heparin; coarse; long range; coarse grained ... See more keywords
A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24709
Abstract: The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with… read more here.
Keywords: solvent accessible; surface area; accessible surface; solvent ... See more keywords
Extension of CAVS coarse‐grained model to phospholipid membranes: The importance of electrostatics
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24770
Abstract: It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse‐grained (CG) model, which has been widely used in simulating… read more here.
Keywords: electrostatics; model; coarse grained; dipole potential ... See more keywords
ESCASA: Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance‐assisted protein structure modeling. I. Backbone and Hβ protons
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26695
Abstract: A method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in nuclear‐magnetic‐resonance (NMR) data‐assisted coarse‐grained simulations of proteins is proposed. In this paper, the… read more here.
Keywords: estimation; nuclear magnetic; magnetic resonance; geometry ... See more keywords
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
Dissecting the general mechanisms of protein cage self‐assembly by coarse‐grained simulations
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4552
Abstract: The development of artificial protein cages has recently gained massive attention due to their promising application prospect as novel delivery vehicles for therapeutics. These nanoparticles are formed through a process called self‐assembly, in which individual… read more here.
Keywords: self assembly; protein cage; general mechanisms; self ... See more keywords
Relationship between the Microstructure and Impact Toughness of the Coarse‐Grained Heat‐Affected Zone for Offshore Engineering Steels with Different Mg Contents
Sign Up to like & getrecommendations! Published in 2021 at "steel research international"
DOI: 10.1002/srin.202100099
Abstract: The relationship between the microstructure and impact toughness of coarse‐grained heat affected zone for offshore engineering steels with 0.0002 and 0.0042 wt% Mg, termed as 2 and 42Mg, respectively, is clarified. With increasing the Mg content… read more here.
Keywords: microstructure impact; impact toughness; coarse grained; grained heat ... See more keywords
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-6406-2_8
Abstract: Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps the most… read more here.
Keywords: dimensional structural; structural properties; properties proteins; one dimensional ... See more keywords
A sumatriptan coarse-grained model to explore different environments: interplay with experimental techniques
Sign Up to like & getrecommendations! Published in 2018 at "European Biophysics Journal"
DOI: 10.1007/s00249-018-1278-2
Abstract: In this work, we developed a coarse-grained model of sumatriptan suitable for extensive molecular dynamics simulations. First, we confirmed the interfacial distribution of this drug in bilayers through cryogenic transmission electron microscopy and small-angle X-ray… read more here.
Keywords: model explore; sumatriptan coarse; model; coarse grained ... See more keywords
Molecular understanding of interactions, structure, and drug encapsulation efficiency of Pluronic micelles from dissipative particle dynamics simulations
Sign Up to like & getrecommendations! Published in 2019 at "Colloid and Polymer Science"
DOI: 10.1007/s00396-019-04535-0
Abstract: AbstractIn this work, we employ coarse-grained dissipative particle dynamics simulations with the hydrogen bonds added explicitly to study the drug encapsulation property, structure, and interactions of Pluronic L64/ibuprofen combinations. The coarse-grained simulations reveal that the… read more here.
Keywords: particle dynamics; drug; coarse grained; dissipative particle ... See more keywords
Extension of coarse-grained UNRES force field to treat carbon nanotubes
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-018-3656-1
Abstract: AbstractCarbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer… read more here.
Keywords: force field; coarse grained; unres force; extension coarse ... See more keywords