Molecular simulations are widely applied in the study of chemical and bio-physical problems. However, the accessible timescales of atomistic simulations are limited, and extracting equilibrium properties of systems containing rare events remains chal...
Determining the drug-target residence time (RT) is of major interest in drug discovery given that this kinetic parameter often represents a better indicator of in vivo drug efficacy than binding affinity. However, obtaining drug-target unbinding rate...
Many natural substances and drugs are radical scavengers that prevent the oxidative damage to fundamental cell components. This process may occur via different mechanisms, among which, one of the most important, is hydrogen atom transfer. The feasibi...
Safe and efficient use of ultrasmall nanoparticles (NPs) in biomedicine requires numerous independent conditions to be met, including colloidal stability, selectivity for proteins and membranes, binding specificity, and low affinity for plasma protei...
Elementary steps and intermediate species of linearly structured biomass compounds are studied. Specifically, possible intermediates and elementary reactions of 15 key biomass compounds and 33 small molecules are obtained from a recursive bond-breaki...
Computational techniques for accurate and efficient prediction of protein-protein complex structures are widely used for elucidating protein-protein interactions, which play important roles in biological systems. Recently, it has been reported that s...
Proteins are classified into families based on evolutionary relationships and common structure-function characteristics. Availability of large data sets of gene-derived protein sequences drives this classification. Sequence space is exponentially lar...
A novel data-based machine learning algorithm for predicting amyloid aggregation rates is reported in this paper. Based on a highly nonlinear projection from 16 intrinsic features of a protein and 4 extrinsic features of the environment to the protei...
As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the time scale of the latent space while inferring a red...
The Debye-Waller factor, a measure of X-ray attenuation, can be experimentally observed in protein X-ray crystallography. Previous theoretical models have made strong inroads in the analysis of beta (B)-factors by linearly fitting protein B-factors f...