Figure 1

The illustration of flexible molecular shape comparison and similarity measure based on the IDSS histograms. Given a molecular shape, the whole process could be divided into three independent steps including sampling (red points) on the molecule, computing inner distances (green line segments) between all sample point pairs, and building the IDSS histogram. Consequently, our approach reduces the similarity measure among molecules to the comparison of IDSS histograms. An example is given for calculating the similarity measure between two different molecules (PDB codes: 1aon-A, 1irk-A), where the similarity score is equal to 0.6535.