Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed together with computationally expensive enhanced sampling methods. Here we show that this sampling inefficiency, which stems from not accounting for the environ...

Virtual screening is one of the most common computer-aided drug design techniques that apply computational tools and methods on large libraries molecules to extract drugs. Ensemble learning a recent paradigm launched improve machine results in terms predictive performance robustness. It has been successfully applied ligand-based virtual (LBVS) approaches. Applying ensemble huge molecular comput...

The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontane...

Model uncertainty hampers consensus on the key determinants of economic growth. Some recent cross-country cross-sectional analyses have employed Bayesian Model Averaging to tackle the issue of model uncertainty. This paper extends that approach to panel data models with countryspecific fixed effects in order to simultaneously address model uncertainty and endogeneity issues. The empirical findi...

Using the theory of machine learning to assist the virtual screening (VS) has been an effective plan. However, the quality of the training set may reduce because of mixing with the wrong docking poses and it will affect the screening efficiencies. To solve this problem, we present a method using the ensemble learning to improve the support vector machine to process the generated protein-ligand ...

Introduction: The inflammatory response requires a coordinated integration of various signaling pathway including cyclooxygenase (COX). COX catalyzes the formation of prostaglandins from arachidonic acid. Among prostaglandins, 15-Deoxy-D12, 14-prostaglandin J2 (15d-PGJ2), an endogenous ligand of Peroxisome proliferator-activated receptor-gamma (PPAR-γ), has been demonstrated to have anti-inflam...

An operational hydrological ensemble forecasting system based on a meteorological ensemble prediction system (M-EPS) coupled with a hydrological model searches to capture the uncertainties associated with the meteorological prediction to better predict river flows. However, the structure of the hydrological model is also an important source of uncertainty that has to be taken into account. This...