84 citations · 239 across the 5 of their papers we have counts for
6 papers
Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations
Narjes Ansari, Zhifeng Francis Jing, Antoine Gagelin +5
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery w…
Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Dhiman Ray, Narjes Ansari, Valerio Rizzi +2
We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived…
Charge gradients around dendritic voids cause nanoscale inhomogeneities in liquid water
Tereza Schonfeldova, Nathan Dupertuis, Yixing Chen +5
Water is the matrix of life and is generally considered a homogeneous, uniform, liquid. Recent experiments report that water is instead a two-state liquid. However, subsequently, t…
Water regulates the residence time of Benzamidine in Trypsin
Narjes Ansari, Valerio Rizzi, Michele Parrinello
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we sim…
The role of water in host-guest interaction
Valerio Rizzi, Luigi Bonati, Narjes Ansari +1
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality…
Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations
Narjes Ansari, Tarak Karmakar, Michele Parrinello
Accurate prediction of a gas solubility in a liquid is crucial in many areas of chemistry, and a detailed understanding of the molecular mechanism of the gas solvation continues to…