100 citations · 218 across the 7 of their papers we have counts for
7 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…
Finding dominant transition pathways via global optimization of action
Juyong Lee, In-Ho Lee, InSuk Joung +2
We present a new computational approach, Action-CSA, to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup act…
Link community detection through global optimization and the inverse resolution limit of partition density
Juyong Lee, Zhong-Yuan Zhang, Jooyoung Lee +2
We investigate the possibility of global optimization-based overlapping community detection, using link community framework. We first show that partition density, the original qual…
Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide
Edward P. O'Brien, John E. Straub, Bernard R. Brooks +1
Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register -sheets, the primary structural component of amyloid fibrils, is a first…
How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins?
E. P. O'Brien, G. Morrison, B. R. Brooks +1
Single molecule Forster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average F…