New developments in force fields for biomolecular simulations
Highlights•Biomolecular force fields (FFs) have progressed rapidly in the past five
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase
properties by force field-based methods require a precise description of the energetics of …
properties by force field-based methods require a precise description of the energetics of …
[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
1.14* CM1A-LBCC: localized bond-charge corrected CM1A charges for condensed-phase simulations
The quality of the 1.14* CM1A and 1.20* CM5 charge models was evaluated for calculations
of free energies of hydration. For a set of 426 neutral molecules, 1.14* CM1A and 1.20* CM5 …
of free energies of hydration. For a set of 426 neutral molecules, 1.14* CM1A and 1.20* CM5 …
Bi2O3 Nanosheets Grown on Carbon Nanofiber with Inherent Hydrophobicity for High-Performance CO2 Electroreduction in a Wide Potential Window
The ever-increasing concern for adverse climate changes has propelled worldwide research
on the reduction of CO2 emission. In this regard, CO2 electroreduction (CER) to formate is …
on the reduction of CO2 emission. In this regard, CO2 electroreduction (CER) to formate is …
Molecular insights into the synergistic mechanisms of hybrid CO2-surfactant thermal systems at heavy oil-water interfaces
A hybrid thermal recovery process is a promising EOR (Enhanced Oil Recovery) method
and has been widely applied to post-steamed heavy oil reservoirs. Due to the complexity of …
and has been widely applied to post-steamed heavy oil reservoirs. Due to the complexity of …
QUBEKit: Automating the derivation of force field parameters from quantum mechanics
Modern molecular mechanics force fields are widely used for modeling the dynamics and
interactions of small organic molecules using libraries of transferable force field parameters …
interactions of small organic molecules using libraries of transferable force field parameters …
Biomolecular force field parameterization via atoms-in-molecule electron density partitioning
Molecular mechanics force fields, which are commonly used in biomolecular modeling and
computer-aided drug design, typically treat nonbonded interactions using a limited library of …
computer-aided drug design, typically treat nonbonded interactions using a limited library of …
Q-Force: Quantum mechanically augmented molecular force fields
The quality of molecular dynamics simulations strongly depends on the accuracy of the
underlying force fields (FFs) that determine all intra-and intermolecular interactions of the …
underlying force fields (FFs) that determine all intra-and intermolecular interactions of the …
Molecular investigation of the self-assembly mechanism underlying polydopamine coatings: the synergistic effect of typical building blocks acting on interfacial …
X Li, C Wu, J Wu, R Sun, B Hou, C Liu… - ACS Applied Materials …, 2024 - ACS Publications
Polydopamine (PDA) is well known as a mussel-inspired adhesive material composed of
oligomeric heteropolymers. However, the conventional eumelanin-like structural assumption …
oligomeric heteropolymers. However, the conventional eumelanin-like structural assumption …