Laboratory Notes

BioShell protocols

  • Clustering poses from ligand docking

Rosetta protocols

  • Preliminary information and input/output file processing
  • How to pick fragments for modeling with Rosetta
  • ab-initio and ab-relax protocols
  • Score patching
  • Docking ligands to P450 enzymes with RosettaScripts

Modeller protocols

  • Homology Modelling that includes ligands

notes on PyMOL

  • Loading input files
  • Selecting stuff
  • Hide & Show
  • Extract, copy or remove
  • Working with electron density
  • Miscellanea

notes on MD simulations with Gromacs

  • How to start an MD simulation
  • Monitoring the progress

Bioinformatic tools

  • Creating a blast database and running blast

Other notes

  • Notes on git
  • Running jobs on a cluster with PBS
Laboratory Notes
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