55 citations · 97 across the 4 of their papers we have counts for
4 papers
Collective Variable for Metadynamics Derived from AlphaFold Output
Vojtěch Spiwok, Martin Kurečka, Aleš Křenek
AlphaFold is a neural-network-based tool for the prediction of 3D structures of protein. In CASP14, a blind structure prediction challenge, it performed significantly better than o…
Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d
Dalibor Trapl, Vojtěch Spiwok
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a grea…
Time-Lagged t-Distributed Stochastic Neighbor Embedding (t-SNE) of Molecular Simulation Trajectories
Vojtěch Spiwok, Pavel Kříž
Molecular simulation trajectories represent high-dimensional data. Such data can be visualized by methods of dimensionality reduction. Non-linear dimensionality reduction methods a…
Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations
Jana Pazúriková, Jaroslav Oľha, Aleš Křenek +1
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten…