Test sets for scoring experiments

In the following sections we compare the performances of PMF scoring functions derived by using different reference states. For doing so we use four different test sets. Set 1 resembles set 1 in Reference 27. It contains 16 serine protease complexes taken from the PDB. The experimental data are taken from Tables 2 and 6 of Eldridge et al. [23] Starting with the highest affinity complex, the following complexes are used: lets, ldwd, letr, lppc, ltmt, lpph, lett, 3ptb, ltnh, 1dwb, ltng, ltnl, lbra, ltni, ltnk. Set 2 of 15 metalloprotease complexes taken from the PDB resembles set 2 in Reference 27. The experimental data are taken from Table 3 of Eldridge et al. [23]. Starting with the highest affinity complex, the following complexes are used: 7cpa, 6cpa, 4tmn, 8cpa, 1mnc, 5tmn, ltlp, ltmn, 5tln, lcbx, 3tmn, 2tmn, 6tmn, 3cpa, 4tln. Set 3 of 17 diverse protein-ligand complexes taken from the PDB resembles set 5 in Reference 27. The experimental data are taken from Tables 1 and 3 of Böhm [20]. Starting with the highest affinity complex, the following complexes are used: 4dfr, lfkf, 4phv, lme, lphg, 2tsc, 2gbp, lrbp, 4hvp, 2cpp, 5cpp, 2xis, 2ifb, 2ypi, lphf, 5can, lmbi. Set 4 resembles

atrim rwifr fiÎRtsncn (A)

Figure 3. An arbitrary set of 12 PMF is shown. The four letter code refers to the atom pair interaction types, where the first two letters refer to the protein and the second two letters to the ligand type (see Reference 27). The two curves per graph belong to PMF derived with Refl and Ref3, respectively. PMF/Ref1 curves are slightly more negative than PMF/Ref3 curves.

atrim rwifr fiÎRtsncn (A)

Figure 3. An arbitrary set of 12 PMF is shown. The four letter code refers to the atom pair interaction types, where the first two letters refer to the protein and the second two letters to the ligand type (see Reference 27). The two curves per graph belong to PMF derived with Refl and Ref3, respectively. PMF/Ref1 curves are slightly more negative than PMF/Ref3 curves.

a set of 63 protein-ligand complexes from the PDB together with reported binding constants assembled by Böhm [40]. It consists ofthe following PDB complexes: lacj, ladd, lbzm, lcbx, 1cil, lcps, lctt, ldwb, ldwc, lela, lelc, 1fkf, lhpv, lhvr, 1183, lldm, lmbi, lphe, lphf, lphg, lppc, lpph, Ipso, lrbp, lrne, lsbp, lsre, ltlp, ltmn, ltnk, lulb, 2cpp, 2ctc, 2er6, 2gbp, 2gpb, 2phh, 2tsc, 2xis, 2ypi, 3cpa, 3dfr, 3ptb, 3tpi, 4dfr, 4er4, 4fab, 4gr1, 4hmg, 4hvp, 4tln, 4tmn, 5cpp, Stim, 5tln, 5tmn, 6can, 6cpa, 6rsa, 7cpa, 7cpp, 9aat, 9hvp.

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