For the Covid Moonshot project, one question by Prof. Frank von Delft of Diamond XChem led to a series of events that culminated in Fragmenstein, a module to do fragment mergers when the followup is as faithful to the starting crystal hits as possible. Even if it's intended use is the hit-to-lead process, there is a nice use that make it rather handy for computational biochemistry in general: switching the ligand in a PDB to another in an energy minimised fashion that obeys the original ligand.
A segfault and NaN driven series of disconnected ideas, analyses and just plain silly posts about computational biochemistry, synthetic biology and microbiology.
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Tuesday, 21 July 2020
Saturday, 4 July 2020
Filling missing loops —the proper way
Previously, I posted about
how to join proteins and add missing loops the shoddy way. Now I'll address how to do it correctly, using Rosetta or Pyrosetta —I am sorry this has been so long overdue.
Since posting this, I realised one can do it even faster by hijacking the threading algorithm, which albeit not it's intended purpose works fine for fixing a structure without supervision —which the following discussed methods do.
Since posting this, I realised one can do it even faster by hijacking the threading algorithm, which albeit not it's intended purpose works fine for fixing a structure without supervision —which the following discussed methods do.