88 citations · 172 across the 5 of their papers we have counts for
5 papers
Protein-protein docking by generalized Fourier transforms on 5D rotational manifolds
Dmitry Padhorny, Andrey Kazennov, Brandon S. Zerbe +7
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current…
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
Olga Kononova, Joost Snijder, Kenneth A. Marx +3
We present a new theory for modeling forced indentation spectral lineshapes of biological particles, which considers non-linear Hertzian deformation due to an indenter-particle phy…
Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico
Olga Kononova, Yaroslav Kholodov, Kelly E. Theisen +5
Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, t…
Langevin dynamics simulations of biomolecules on graphics processors
A. Zhmurov, R. I. Dima, Y. Kholodov +1
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules,…
Efficient pseudo-random number generators for biomolecular simulations on graphics processors
A. Zhmurov, K. Rybnikov, Y. Kholodov +1
Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent, widely used to access the microscopic transitions in biomolecules, require a reliab…