Alignment to an inhibitor in MarvinSpace

tutorial · 8 years ago
by Adrián Kalászi (ChemAxon)
MarvinSpace
Alignment of a molecule to a thrombin inhibitor (1DWC) with MarvinSpace. 3d coordinates of the molecule to align is generated automatically if there was none found. The conformation of the molecule is tweaked so as to adapt the most to the original ligand. The protein surroundings are not considered yet. Usage:
  • select the original ligand
  • highlight the molecule to align
  • press the smiley icon on toolbar
Hint: on the sidebar select the "popup \ edit the the ligand with marvin sketch" and correct the possible bond order issues in the pdb file.