Matching & Docking EM Maps Figure 2. Examples of low-to-low resolution matching and docking. The top ranking matches are shown, obtained in FitEM2EMIN scans that employ w values calculated from the dependency graph in Figure 1. EM envelopes are shown in yellow. The DifferenceGrid portions where object A protrudes out of object B are colored as object A, and vise versa for object B. The individual images were prepared with the software package Amira and are not to scale. Details for each row of pictures are listed from left to right. (A) Matching of two EM structures of the DnaB.DnaC complex (top and side views). Shown are the EM envelope of objects A (resolution 42.2 A˚ ); the virtual atoms representation of object B (resolution 26 A˚ ) in red within its EM envelope; the identity match (score 1963, ranked 1); match deviating by 6u (score 1352, ranked 4); match deviating by 12u (score 96, ranked 7). (B) The virtual atoms representations of GroES-ADP7-GroEL-ATP7 (blue) and GroEL-ATP7 (red) within their EM envelopes; top and side views of the DifferenceGrid results. (C) Virtual atoms representations of AMPPNP-TClpB (blue), ATP-TClpB mutant (red) and ADP-TClpB (cyan); top views of the DifferenceGrid results for the match of AMPPNP-TClpB to ATP-TClpB mutant and for the match of ATP-TClpB mutant to ADP-TClpB; sections through the side views of the DifferenceGrid results for the same matches. (D) Virtual atoms representations of the 80S ribosome (blue) and the 40S subunit (red); the top ranking match and the DifferenceGrid results. (E) Side and bottom views of the top ranking docking model between Kv4.2*- KChlP2 (blue) and the simulated map of b24 (red); changes in the complementarity score as function of y, the rotation angle about the 4-fold axis of the predicted complex. doi:10.1371/journal.pone.0003594.g002 match with a negative score is ranked 39 (see Table 2). Figure 2A presents the correct top ranking match and additional matches deviating by 6u or 12u. The GroEL/GroES chaperonin complex is a molecular machine whose components assembly and disassembly upon ATP binding and hydrolysis is accompanied by conformation changes. GroEL consists of two 7-subunits rings, which can be in the apo state or loaded with either ATP or ADP; GroES consists of a single 7-subunits ring. The structures of the complexes GroES- ADP7-GroEL-ATP7 [27] and GroES-ATP7-GroEL [28], which were determined at very different resolutions (23.5 and 7.7 A˚), are expected to be similar [28]. Our algorithm matched these objects correctly, ranking a correct match at the top. We then matched GroEL-ATP7 [27] to GroES-ADP7-GroEL-ATP7 [27] and the PLoS ONE | www.plosone.org 4 October 2008 | Volume 3 | Issue 10 | e3594