Fragment docking : how to select the correct pose ?

In this tutorial, we will use a novel knowledge-based method which is applicable to scoring of fragment docking poses.

The method, named LID for Local Interaction Density, builds a consensus interaction map from all experimental observations. All reference complexes are 3D-aligned in a common frame, then the density of interactions is encoded into a grid. Docking pose are scored from the matching of fragment atoms to the grid.

Here we asked whether information on binding mode can help selecting the correct pose of fragments docked into human carbonic anhydrase II (HCA II).


The complete tutorial material is available from the USB key. It can be downloaded also here :

The archive uncompresses itself into a directory named lid_tutorial. The architecture of directories and files in this directory is important for the tutorial to work well.

Step-by-step instructions

The protocol of the tutorial session is available in the following document :