SCORING FUNCTION FOR MOLECULAR ALIGNMENT J. Chem. Inf. Model., Vol. 50, No. 9, 2010 1729 Figure 3. Rigid-body alignment of 3TMN onto 5TLN (carbons in green). Carbons of the correct answer for 3TMN are in dark blue. Carbons of our solutions (top and bottom are best and second best scoring, respectively) are in cyan. by optimizing the score. When we did this with many starting poses, we found that we ended up with fewer resulting aligned poses when we used smaller values of R (unpublished results). This is in line with our expectation that smaller values of R smooth out the score landscape. According to previous works of Gaussian function-based alignment scores, values of R of between 0.1 and 0.5 Å-2 were found to be reasonable.4,16,19,20 In light of this, we alignment mode method CDK2 HIV P38 ESR1 trypsin rhinovirus ROCS 30% 39% 27% 44% 57% 50% rigid FLEXS 25% 24% 27% 47% 73% 52% Figure 4. Important pharmacophore features for the CDK2 ligands include two hydrogen-bond donors (magenta sphere) and one acceptor (cyan sphere). tried out a total of 7 values for Ra, from 0.06 to 0.7 Å-2. The corresponding numbers of good poses among the top 25 are tabulated in Table 2a. It can be seen that for the values of Ra tested, a value of 0.5 Å-2 was the best, with an average of 4.83 good poses among the top 25. After establishing a value for Ra, the relative weights of the atom-based terms were optimized one by one. We ﬁrst looked at the weight wDA for the hydrogen-bonding atoms (donor and acceptor) similarity terms (T1 and T2 in Table 1). For this we tried out 7 values for wDA, from 0.5 to 32, in logarithmic intervals. The corresponding numbers of good poses among the top 25 are tabulated in Table 2b. A value of 4 turned out to be the most favorable, with an average of 6.10 good poses among the top 25. After this, we turned to the similarity term between hydrophobic atoms (T3 in Table 1). Besides trying to establish the optimal weight wHH for this term, we also tried out two schemes of deﬁning hydrophobic atoms. One used the conventional hydrophobic atom assignment in MOE.22 The other scheme was based on how far topologi- cally an atom was from any hydrogen-bonding atom. Atoms that were two or more bonds away from any hydrogen-bond acceptors or donors were considered hydrophobic. Tables 2c and 2d give the numbers of good poses among the top 25 for various values of wHH using the two schemes. It can be seen that the two schemes gave very similar results, with the optimal weighting factor wHH to be around 1.0 for both schemes. current 40% 85% 43% 59% 80% 50% ROCS 20% 6% 22% 25% 55% 50% ﬂexible FLEXS 21% 8% 24% 28% 29% 50% current 22% 16% 30% 41% 61% 50% Table 5. Percentage of Correct Results Given by the Current Scoring Function Compared to Those from Two Published Methodsa a For each of the six systems, pairwise cross-alignments were carried out for all n × n ligand pairs, where n is the number of ligands in the system. If the top scoring result yielded an rmsd of under 2 Å for the heavy atoms, then it was considered correct. This table gives the percentage of correct results for the n × n ligand pairs in the system, as reported on Table 2a of Chen et al.23