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physics.bio-ph2024
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…
physics.bio-ph2024
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…