Artificial intelligence (AI)-based approaches have had indubitable impact across the sciences through the ability to extract relevant information from raw data. Recently, AI has also found use in enhancing the efficiency of molecular simulations, whe...
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...
MOTIVATION: Partial atomic charges are usually used to calculate the electrostatic component of energy in many molecular modeling applications, such as molecular docking, molecular dynamics simulations, free energy calculations and so forth. High-lev...
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...
MOTIVATION: Protein structure refinement is an important step of protein structure prediction. Existing approaches have generally used a single scoring function combined with Monte Carlo method or Molecular Dynamics algorithm. The one-dimension optim...
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...
MOTIVATION: Protein structure refinement aims to bring moderately accurate template-based protein models closer to the native state through conformational sampling. However, guiding the sampling towards the native state by effectively using restraint...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
In the analysis of protein-ligand interactions, two abstractions have been widely employed to build a systematic approach to analyze these complexes: protein and chemical spaces. The pioneering idea of the protein space dates back to 1970, and the ch...
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