249 citations · 928 across the 13 of their papers we have counts for
3 papers · 1 filter
High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets
Hythem Sidky, Wei Chen, Andrew L. Ferguson
State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajec…
Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration
Wei Chen, Andrew L Ferguson
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamic…
Spin models inferred from patient data faithfully describe HIV fitness landscapes and enable rational vaccine design
Karthik Shekhar, Claire F. Ruberman, Andrew L. Ferguson +3
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Kno…