Fig. 1

Example of pose generation error. Top: crystal structure of PI3K α in complex of a tetrahydropyrazolo[1,5-a]pyrazine codenamed 3K6 (PDB ID: 4WAF). Bottom: re-docked pose of 3K6, generated by idock [2]. Hydrogen bonds are rendered as dashed cyan lines, and π stackings are rendered as dashed pink lines. The RMSD (Root-Mean Square Deviation) between the co-crystallised pose and the re-docked pose of 3K6 is 1.15 Å, which is a quantitative measure of pose generation error. These two plots were created by iview [17], an interactive WebGL visualizer that circumvents the requirement of Java, yet supports the construction of macromolecular surface and the display of virtual reality effects and molecular interactions. iview is freely available at http://istar.cse.cuhk.edu.hk/iview/