William Sinko

TL;DR: In this paper, the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage were systematically compared.

TL;DR: A number of recent advances in computer-aided drug discovery techniques that have been proposed to incorporate receptor flexibility into structure-based drug design help to improve the accuracy of methods used to estimate binding affinities and can contribute to the discovery of novel drug leads.

TL;DR: Modifications to standard rigid receptor docking algorithms are investigated and the combination of free energy calculations and enhanced sampling techniques are explored, which may help improve the efficiency of drug discovery and development.

TL;DR: The discovery and X-ray crystallographic structures of 10 chemically diverse compounds that inhibit bacterial undecaprenyl diphosphate synthase, an essential enzyme involved in cell wall biosynthesis, provide numerous leads for antibacterial development and open up the possibility of restoring sensitivity to drugs such as methicillin, using combination therapies.

TL;DR: A scaled molecular dynamics method is proposed, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations, which is comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in re weighting.