26 citations · 41 across the 2 of their papers we have counts for
3 papers
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…
q-bio.BM2011
Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations
Lukasz Peplowski, Mateusz Sikora, Wieslaw Nowak +1
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks sho…