Homology-Modeled 3D Structure of NDM-1 A total of 100 homology-modeled structures for NDM-1 were derived with each having a C-score. The C-score is a ''confidence score'' for estimating the quality of a computed model: a high Cscore signifies a model with a high confidence and vice-versa. Shown in Fig. 2A is the structure with the highest C-score that was used as a receptor for further docking studies. Meanwhile, we employed PROCHECK [52] to estimate the quality of our models. It was indicated by PROCHECK that there are 93.1% residues located in the ''core'' and ''allowed'' regions, 4.6% in the ''general'' region and only 2.3% in the ''disallowed'' regions ( Fig.  S1 ). In the computational structure, all the bond lengths for the main-chain residues and 91.9% bond angles for the main-chain residues are within the allowed limits. To further examine our computational model of NDM-1, we also used the tool of QMEAN, which is a scoring function of a linear combination of 6 structural descriptors [53] . The QMEAN score ranges between 0 and 1 with higher value to reflect a better quality of the model. The QMEAN score for the current computational model is 0.67, and the density plot of this QMEAN score is shown in Fig. S2 . To evaluate the absolute model quality, we also calculated a Z-score of the computational model in comparison with the scores of the reference X-ray structures of similar size from the Protein Data Bank (Fig. S3) . For each of the QMEAN components, a Z-score was computed in comparison with the average X-ray structures (the average value is 0, as shown in Fig. S4 ). Based on these analyses, we further examined the per-residue error (Fig. S5) , visualized using a color gradient from blue (reliable regions with estimated error below 1 Å ) to red (potentially unreliable regions with estimated error above 3.5 Å ). We found that the residues in the potentially unreliable regions were mainly located on the loop regions in the computational model, indicating that further molecular dynamics optimizations are needed, as described below.