GitHub Projects

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Here are a few of my public repositories:

• KNNAS
  The kNN-AS algorithm and the experiments performed to evaluate exploration in artificial landscapes and Adenylate Kinase conformational space in comparison to full MD and MAREAP.

• KNNAS-PROTAC
  The kNN-AS algorithm used in a pipeline where MD simulations are run with GROMACS and the conformational landscape is described by convolutional variational autoencoders. The process automatically submits jobs to the queue and keeps track of the processes. This allows for running the algorithm on scale for multiple PROTAC systems to evalute the conformational landscape with MSM models.

• PROTAC ternary complex benchmark
  All the files for the PROTAC ternary complex prediction benchmark and instruction on how to run protocols in ICM, MOE and PRosettaC.