A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

The use of molecular simulation to estimate the strength of macromolecular binding free
energies is becoming increasingly widespread, with goals ranging from lead optimization …

The presentation of potentially pathogenic peptides by major histocompatibility complex
(MHC) molecules is one of the most important processes in adaptive immune defense …

The purpose of statistical mechanics is to provide a route to the calculation of macroscopic
properties of matter from their constituent microscopic components. It is well known that the …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …

The accurate prediction of the binding affinity changes of drugs caused by protein mutations
is a major goal in clinical personalized medicine. We have developed an ensemble-based …

The EGF receptor (EGFR) regulates important cellular processes including proliferation,
differentiation, and apoptosis. EGFR is frequently overexpressed in a range of cancers and …

结合分子动力学(molecular dynamics, MD) 和半经验量子力学(semi-empirical quantum
mechanics, DFT) 的分子模拟方法, 研究了水分对绝缘纸微观特性的影响. 采用Theodorou …

T lymphocytes are stimulated when they recognize short peptides bound to class I proteins
of the major histocompatibility complex (MHC) protein, as peptide–MHC complexes. Due to …