What are some good tools for structural alignment of pdb ligand molecules?

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Yoshinobu Ishikawa

Hi,

VMD and DS visualizer should be nice for you.

http://www.ks.uiuc.edu/Research/vmd/

http://chembytes.wdfiles.com/local--files/vmd/vmd-basic_tutorial-1_0.pdf

http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php

http://www.adrianomartinelli.it/Fondamenti/Tutorial_0.pdf

https://pharminfo.univie.ac.at/uploads/media/Discovery_Studio_Tutorial.pdf

Hi again,

MGL Tools and MarvinSpace are also nice.

http://mgltools.scripps.edu/downloads

http://pmvbase.blogspot.jp/2010/06/aligning-small-molecules.html

https://www.chemaxon.com/download/marvin-suite/

https://www.chemaxon.com/products/marvin/marvinspace/

Vishal Pandya

Use Pymol. Very easy to handle and tweak around.