To allow a quantitative comparison, we calculated the minimum Cor root mean square deviation ( RMSD ) distance between members of the cluster of dimeric complexes that formed during the simulations and each crystal structure listed in 82 Table.

The calculated RMSD values of S3 and S4 Tables suggest that the dimer interface from simulations that is closest to one inferred from crystal structures is the TM1,2,H8/TM1,2,H8 interface.

The relatively small RMSD values listed in S3 Table, indicate that the simulations of the 5-OR system also reproduced both symmetric and asymmetric dimer interfaces inferred from CXCR4 crystal structures [24] (see S2 Table for details) with reasonable accuracy.

Comparisons with available crystal structures of parallel interacting GPCRs (see 82 Table for a current list) were evaluated by calculating the overall COL RMSD .

For the evaluation of the identified hetero-dimeric interfaces, both pair combinations (e.g., u-OR/S-OR and 5-OR/u-OR) were considered for the superposition onto crystal structures, and the RMSD was defined as the minimum between the two individual RMSD values.

Minimum RMSD distances (below 10 A) between homo-dimeric complexes formed during simulation and selected crystal structures.

For each cluster of dimeric complexes that formed during simulation, the configuration corresponding to the lowest RMSD (highlighted in bold) is depicted in Figs.

Notably, the root mean square deviation ( RMSD ) of this loop conformation from the resolved loop of the newest high-resolution crystal structure of 5-OR [40] is 0.46 A overall.

To test whether the chemical and physical properties evaluated by PocketFEATURE are captured by traditional structural-only metrics such as RMSD, we calculated the RMSD of the 20 pocket residues aligned to the same 20 residues of the 4DXD SaFtsZ-PC190723 co-crystal structure for each MD trajectory (Fig.

Large-magnitude pocket scores did not correspond with low RMSD from the SaFtsZ-PC190723 co-crystal, with SaFtsZ and SeFtsZ having values intermediate between the low values of APO SaFtsZ and BsFtsZ and the high values of SaFtsZG193D.

Our results establish that PocketFEATURE is able to not only distinguish aspects of the drug-binding pocket in FtsZ structures from different species that are not evident from methods such as RMSD , which only considers structural information; the algorithm also can evaluate how protein pockets in molecules from resistant mutants may differ from the optimal binding structure.

Root mean squared deviation ( RMSD ) of the pockets of the crystal structures to the pocket of the SaFtsZ-PC190723 co-crystal (Fig.

2B) clearly identified that Staphylococcus species have pocket structures that are more similar to that of the SaFtsZ-PC190723 co-crystal, but in contrast to PocketFEATURE, RMSD is unable to distinguish among non-Staphylococcus species.

(B) RMSD of the 3D coordinates of FtsZ crystal structures from the P0190723 co-crystal coarsely separate the proteins into close and distant relations of GDP-bound Staphylococcus FtsZ, but this measurement does not capture additional features of the drug pockets that distinguish between structures of medium and low similarity to the SaFtsZ-PC1 90723 co-crystal.

Calculation of the root mean square displacement (RMSD) of the protein during the simulation revealed a sharp increase of the protein RMSD at the beginning of the simulations to ~ 0.35 nm.

The RMSD for the longer AT-MD simulations subsequently increased to final values of ~ 0.5 nm (89A Fig).

Root mean square deviation ( RMSD ) and the closed state of UraA.

Root mean square deviation ( RMSD ) of UraA as a function of the simulation time for the atomistic systems (UraA-AT in PE, PG, CL, UraA-pc-AT in PC and UraA-pe-AT in PE in Table 1 and 81 Table).