Polarisable force fields: what do they add in biomolecular simulations?
Highlights•Induced polarisation is an essential component of biomolecular interactions like
cation-pi, hydrogen bonding, and ionic interactions.•Advances in simulation algorithms and …
cation-pi, hydrogen bonding, and ionic interactions.•Advances in simulation algorithms and …
Biomolecular modeling and simulation: a prospering multidisciplinary field
We reassess progress in the field of biomolecular modeling and simulation, following up on
our perspective published in 2011. By reviewing metrics for the field's productivity and …
our perspective published in 2011. By reviewing metrics for the field's productivity and …
AMOEBA polarizable atomic multipole force field for nucleic acids
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …
and electrostatic parameters were determined from high-level quantum mechanical data …
AMOEBA+ classical potential for modeling molecular interactions
Classical potentials based on isotropic and additive atomic charges have been widely used
to model molecules in computers for the past few decades. The crude approximations in the …
to model molecules in computers for the past few decades. The crude approximations in the …
Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins
Calcium ion is a versatile messenger in many cell-signaling processes. To achieve their
functions, calcium-binding proteins selectively bind Ca2+ against a background of …
functions, calcium-binding proteins selectively bind Ca2+ against a background of …
Thermodynamics of Metal–Acetate Interactions
Metal ions play crucial roles in protein-and ligand-mediated interactions. They not only act
as catalysts to facilitate biological processes but are also important as protein structural …
as catalysts to facilitate biological processes but are also important as protein structural …
[HTML][HTML] SAPT codes for calculations of intermolecular interaction energies
Symmetry-adapted perturbation theory (SAPT) is a method for calculations of intermolecular
(noncovalent) interaction energies. The set of SAPT codes that is described here, the current …
(noncovalent) interaction energies. The set of SAPT codes that is described here, the current …
Plummeting toxic contaminates from water through phycoremediation: Mechanism, influencing factors and future outlook to enhance the capacity of living and non …
Freshwater habitats hold a unique role in the survival of all living organisms and supply
water for drinking, irrigation, and life support activities. In recent decades, due to …
water for drinking, irrigation, and life support activities. In recent decades, due to …
On the computational characterization of charge-transfer effects in noncovalently bound molecular complexes
Charge-transfer (CT) is an important binding force in the formation of intermolecular
complexes, and there have been a variety of theoretical models proposed to quantify this …
complexes, and there have been a variety of theoretical models proposed to quantify this …
Classical exchange polarization: An anisotropic variable polarizability model
Polarizability, or the tendency of the electron distribution to distort under an electric field,
often depends on the local chemical environment. For example, the polarizability of a …
often depends on the local chemical environment. For example, the polarizability of a …