Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues
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DOI: 10.1002/jcc.24519
Abstract: Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was… read more here.
Keywords: continuum solvent; pka shifts; force field; continuum ... See more keywords
Parameterization of the GPR119 Receptor Agonist AR231453
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25079
Abstract: The GPR119 receptor is a class A G protein‐coupled receptor expressed mainly in pancreatic beta cells. Since GPR119 receptor activation ameliorates Type 2 Diabetes through an increase in glucose‐dependent insulin release, the development of new… read more here.
Keywords: force field; agonist; parameterization gpr119; gpr119 receptor ... See more keywords
A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25850
Abstract: Peptoids, or poly‐n‐substituted glycines, are peptide‐like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of self‐assembling structures based on the type and sequence of the side… read more here.
Keywords: cis trans; force field; side chains;
MembrFactory: A Force Field and composition Double Independent Universal Tool for Constructing Polyamide Reverse Osmosis Membranes
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26015
Abstract: The topmost polyamide (PA) layer of the thin‐film‐composite reverse osmosis (RO) membrane is the most important part in the membrane‐based RO technology. With the aid of molecular dynamics simulations, many PA layer‐related features in the… read more here.
Keywords: reverse; membrfactory force; force field; reverse osmosis ... See more keywords
Modeling the effect of ion‐induced shock waves and DNA breakage with the reactive CHARMM force field
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26399
Abstract: Ion‐induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated… read more here.
Keywords: force field; induced shock; ion; reactive charmm ... See more keywords
Automation of AMOEBA polarizable force field for small molecules: Poltype 2
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DOI: 10.1002/jcc.26954
Abstract: A next‐generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using… read more here.
Keywords: polarizable force; free energy; torsion; small molecules ... See more keywords
Benchmarking biomolecular force field‐based Zn2+ for mono‐ and bimetallic ligand binding sites
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27052
Abstract: Zn2+ is one of the most versatile biologically available metal ions, but accurate modeling of Zn2+‐containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn2+ models are parameterized in bulk solvent,… read more here.
Keywords: ligand binding; biomolecular force; zn2 models; force field ... See more keywords
Adaptation of reach action to a novel force-field is not predicted by acuity of dynamic proprioception in either older or younger adults
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DOI: 10.1007/s00221-020-05997-3
Abstract: Healthy ageing involves degeneration of the neuromuscular system which impacts movement control and proprioception. Yet the relationship between these sensory and motor deficits in upper limb reaching has not been examined in detail. Recently, we… read more here.
Keywords: force field; field; age; adaptation ... See more keywords
Modeling of adsorption of CO2 in the deformed pores of MIL-53(Al)
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DOI: 10.1007/s00894-017-3281-4
Abstract: Molecular simulations were performed to predict CO2 adsorption in flexible metal-organic frameworks (MOFs). A generic force field was fitted to our experimental data to describe the non-bonded (electrostatic and van der Waals) interactions between CO2… read more here.
Keywords: adsorption; force field; co2 deformed; co2 ... See more keywords
Development of an AMBER-compatible transferable force field for poly(ethylene glycol) ethers (glymes)
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-017-3355-3
Abstract: AbstractAn all-atom force field consistent with the general AMBER force field (GAFF) format for poly(ethylene glycol) dimethyl ether (diglyme or G2) was developed by fitting to experimental liquid densities and dielectric constants. Not surprisingly, the… read more here.
Keywords: force; poly ethylene; force field; ethylene glycol ... See more keywords
Modeling DMPC lipid membranes with SIRAH force-field
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DOI: 10.1007/s00894-017-3426-5
Abstract: Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the… read more here.
Keywords: lipid membranes; force field; dmpc lipid; sirah force ... See more keywords