End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Water models for biomolecular simulations
AV Onufriev, S Izadi - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …
function rely heavily on a variety of methods—water models—to approximate the influence …
Omicron BA. 2 (B. 1.1. 529.2): high potential for becoming the next dominant variant
The Omicron variant has three subvariants: BA. 1 (B. 1.1. 529.1), BA. 2 (B. 1.1. 529.2), and
BA. 3 (B. 1.1. 529.3). BA. 2 is found to be able to alarmingly reinfect patients originally …
BA. 3 (B. 1.1. 529.3). BA. 2 is found to be able to alarmingly reinfect patients originally …
Quantitative toxicity prediction using topology based multitask deep neural networks
The understanding of toxicity is of paramount importance to human health and
environmental protection. Quantitative toxicity analysis has become a new standard in the …
environmental protection. Quantitative toxicity analysis has become a new standard in the …
Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …
Biomolecular electrostatics and solvation: a computational perspective
An understanding of molecular interactions is essential for insight into biological systems at
the molecular scale. Among the various components of molecular interactions, electrostatics …
the molecular scale. Among the various components of molecular interactions, electrostatics …
An interface-fitted mesh generator and virtual element methods for elliptic interface problems
A simple and efficient interface-fitted mesh generation algorithm which can produce a semi-
structured interface-fitted mesh in two and three dimensions quickly is developed in this …
structured interface-fitted mesh in two and three dimensions quickly is developed in this …
A new weak Galerkin finite element method for elliptic interface problems
A new weak Galerkin (WG) finite element method is introduced and analyzed in this paper
for solving second order elliptic equations with discontinuous coefficients and interfaces …
for solving second order elliptic equations with discontinuous coefficients and interfaces …
Poisson–boltzmann–nernst–planck model
Q Zheng, GW Wei - The Journal of chemical physics, 2011 - pubs.aip.org
The Poisson–Nernst–Planck (PNP) model is based on a mean-field approximation of ion
interactions and continuum descriptions of concentration and electrostatic potential. It …
interactions and continuum descriptions of concentration and electrostatic potential. It …
A topological approach for protein classification
Protein function and dynamics are closely related to its sequence and structure. However,
prediction of protein function and dynamics from its sequence and structure is still a …
prediction of protein function and dynamics from its sequence and structure is still a …