289 citations · 345 across the 3 of their papers we have counts for
3 papers
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules
Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda +1
Finding low dimensional representation of data from long-timescale trajectories of biomolecular processes such as protein-folding or ligand-receptor binding is of fundamental impor…
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders
Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda +1
Conformational sampling of biomolecules using molecular dynamics simulations often produces large amount of high dimensional data that makes it difficult to interpret using convent…
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald +11
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark…