44 citations · 210 across the 12 of their papers we have counts for
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physics.bio-ph2015★ 15 cited
Entropic measure to prevent energy over-minimization in molecular dynamics simulations
Jakub Rydzewski, Rafal Jakubowski, Wieslaw Nowak
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied…
physics.chem-ph2015★ 26 cited
Memetic Algorithms for Ligand Expulsion from Protein Cavities
Jakub Rydzewski, Wieslaw Nowak
Ligand diffusion through proteins is a fundamental process governing biological signaling and enzymatic catalysis. The complex topology of protein tunnels results in difficulties w…