Resolution limit of data-driven coarse-grained models spanning chemical space
Kiran H. Kanekal and Tristan Bereau, Journal of Chemical Physics (2019)
Building alternative CG Martini models
Building alternative CG Martini models
Importance sampling and machine learning across chemical space
Using high-throughput drug-membrane free-energy calculations to explore the Meyer-Overton rule
Structure-property relationships of drug-membrane permeability
Structured-based coarse-graining rescues one out of two dynamical regimes
Short review on data-driven methods in soft-matter simulations
Structural-kinetic-thermodynamic relationships for peptide models
Polymer crystal polymorphs from atomistic and coarse-grained simulations
Review on characterizing proteins at interfaces
Intermolecular interactions across chemistry from physics-based models and machine learning
Structural-kinetic relationships and links to conformational entropy
High-throughput free-energy calculations of drug-membrane thermodynamics
Impact of nitrated fatty acids on membrane properties
Improve coarse-grained model by optimizing both its statics and kinetics
Kinesin-like motion from a simple biomimetic construct
Challenges in modeling the backbone in CG models
Electrostatic impact of the sigma hole on neighboring atoms
Data-driven approaches in soft matter
Biased Markov state models to improve simulation kinetics
We compare thermodynamic properties of a transmembrane helix between coarse-grained and atomistic models
Multi-timestep integrator for NVT and NPT simulations; implementation in ESPResSo
Parametrization of conformationally-dependent atomic multipoles without explicit QM calculation
Quickly parametrizing the Martini force field of small organic molecules
Influence of fluorine on solvent dynamics from atomistic simulations with multipoles and 2D-IR spectroscopy
Effects of multipole electrostatics on the surrounding solvent dynamics
Folding simulations of small peptides and proteins in the membrane
Many-body van der Waals interaction energies without electron density
Improved 2DIR measurements using multipole electrostatics for NMA
Coarse-grained peptide-lipid model without explicit secondary-structure bias
Condensed-phase simulations with static atomic multipoles
Run and analyze simulations with different force-field resolutions
Effects of symmetry in the stability of contacting protein-capsid strands
Insight into protein folding cooperativity from a micranonical analysis
Ph.D. thesis on protein coarse-graining
Link between secondary and tertiary structure formation in protein folding
Faster convergence of the Weighted Histogram Analysis Method
Coarse-grained model for alpha-helix and beta-sheet folding