533 citations · 1.9k across the 55 of their papers we have counts for
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Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE
Xinyu Gu, Akashnathan Aranganathan, Pratyush Tiwary
Small molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo stru…
An Information Bottleneck Approach for Markov Model Construction
Dedi Wang, Yunrui Qiu, Eric Beyerle +2
Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the comple…
Exploring kinase DFG loop conformational stability with AlphaFold2-RAVE
Bodhi P. Vani, Akashnathan Aranganathan, Pratyush Tiwary
Kinases compose one of the largest fractions of the human proteome, and their misfunction is implicated in many diseases, in particular cancers. The ubiquitousness and structural s…
Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck
Shams Mehdi, Dedi Wang, Shashank Pant +1
An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires a priori knowledge of the approximate reaction coordinate describing the rel…
Ligand dissociation mechanisms from all-atom simulations: Are we there yet?
Joao Marcelo Lamim Ribeiro, Sun-Ting Tsai, Debabrata Pramanik +2
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein comp…