Unsupervised learning is becoming an essential tool to analyze the increasingly large amounts of data produced by atomistic and molecular simulations, in material science, solid …
Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost …
A Barducci, M Bonomi… - Wiley Interdisciplinary …, 2011 - Wiley Online Library
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics simulations and reconstructing the free‐energy surface as a function of few selected …
The accurate resolution of the binding mechanism of a ligand to its molecular target is fundamental to develop a successful drug design campaign. Free-energy calculations …
It is increasingly appreciated that the rates at which drugs associate with and dissociate from receptors—the binding kinetics—directly impact drug efficacy and safety. The molecular …
Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic understanding of large …
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and …
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been …