Quantifying the Single-Cell Morphological Landscape of Cellular Transdifferentiation through Force Field Reconstruction.
Sign Up to like & getrecommendations! Published in 2025 at "Advanced science"
DOI: 10.1002/advs.202512325
Abstract: Advancements in sequencing technologies have reshaped our understanding of cell behaviors through transcriptomics, but a gap remains in developing quantitative models for multi‐omic data, especially for cellular morphology changes. A pivotal challenge is the lack… read more here.
Keywords: cell; force field; landscape; single cell ... See more keywords
Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
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
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
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
Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK‐Based Force Field Library
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.70071
Abstract: Computational chemistry plays a crucial role in drug design and development, where accurate modeling of molecular interactions is vital in rational drug design. Among the available methods, force fields such as MMFF94 are extensively used… read more here.
Keywords: chemistry; energy; robust; jmolecular energy ... See more keywords
Development of a New AMBER Force Field for Cysteine and Histidine Cadmium‐Binding Proteins and Its Validation Through QM/MM MD Simulations
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.70154
Abstract: We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of cadmium(II)‐binding proteins. The proposed force field takes into account the polarization effect produced by the central… read more here.
Keywords: binding proteins; force; force field; cadmium binding ... 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
Sign Up to like & getrecommendations! Published in 2020 at "Experimental Brain Research"
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