Polarizable force fields for biomolecular simulations: Recent advances and applications
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics,
including electronic polarization. Due to recent advances in physical models, simulation …
including electronic polarization. Due to recent advances in physical models, simulation …
CHARMM at 45: Enhancements in accessibility, functionality, and speed
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
Critical knowledge gaps in mass transport through single-digit nanopores: A review and perspective
Not all nanopores are created equal. By definition, nanopores have characteristic diameters
or conduit widths between∼ 1 and 100 nm. However, the narrowest of such pores, perhaps …
or conduit widths between∼ 1 and 100 nm. However, the narrowest of such pores, perhaps …
Parameterization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models
Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
[HTML][HTML] A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
E Duboue-Dijon, M Javanainen, P Delcroix… - The Journal of …, 2020 - pubs.aip.org
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …
processes, which are often hardly accessible to experiment. However, the results of the …
The oxytocin signaling complex reveals a molecular switch for cation dependence
JG Meyerowitz, MJ Robertson… - Nature Structural & …, 2022 - nature.com
Oxytocin (OT) and vasopressin (AVP) are conserved peptide signaling hormones that are
critical for diverse processes including osmotic homeostasis, reproduction, lactation and …
critical for diverse processes including osmotic homeostasis, reproduction, lactation and …
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 …
Automation of AMOEBA polarizable force field for small molecules: Poltype 2
A next‐generation protocol (Poltype 2) has been developed which automatically generates
AMOEBA polarizable force field parameters for small molecules. Both features and …
AMOEBA polarizable force field parameters for small molecules. Both features and …
SARS-CoV-2 fusion peptide has a greater membrane perturbating effect than SARS-CoV with highly specific dependence on Ca2+
AL Lai, JH Freed - Journal of Molecular Biology, 2021 - Elsevier
Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human
pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry …
pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry …
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 …