For small peptides such as Ile-Val (system C and Cw) and Gly-Tyr (system D), RMSD values <1.0 Å (Figs. 1a, 2a, Fig. 2.) and 1.5 Å (Fig. 1b), respectively, were achieved. Moreover, the lowest energy conformations of 100 out of 500 docking trials were the members of the subclasses in all cases. The occupancies (N) of the classes and their subclasses were lower, than those of C, Cw, and D in Table 2. This is owing to the larger number of degrees of freedom of the ligand: The search algorithm was used not only for finding the correct binding position/orientation but also for searching the conformation of the ligand in this case. Therefore, the number N of successful docking trials was lower. For Ile-Val, both solvated (Cw) and water-free (C) targets were used. The presence of water molecules right above the binding site did not hinder docking to the site: The occupancies N were smaller, but the Edocked values were lower than in the case of “dry” protein. This trend was found also for the crystal energies and the Edocked values of rigid ligands owing to interactions with the water molecules (Tables 1, 2, Table 2.). In system B, the real binding position of the loop was found only in the second class. This limited success is caused by the length of the peptide fragment that was used as a ligand (for details, see Rigid Ligands section). Tripeptides, such as Gly-Ala-Trp (system E; Fig. 2b) and Ace-Ala-Pro-Tyr (system F; Fig. 1c), were also docked successfully to their respective pockets (Table 3). The Gly-Ala-Trp (γ-chymotrypsin) system is a difficult task for docking calculations. The crystal structure of this complex (Harel et al. 1991) contains an average structure of a covalently bound ligand and a nonbonded complex. Obviously, the molecular mechanics-based docking technique is developed for only nonbonded interactions. Despite the problematic crystal structure, the hydrophobic pocket (the most important part of the binding site, see Fig. 2b) of γ-chymotrypsin was identified reproducibly. Together with system B, the latter example proves the robustness of the method: The binding location was found even when only part of the ligand or of the site was defined properly. In the complex of SG protease and Ace-Pro-Ala-Pro-Tyr (system I), the first Pro residue of the peptide has no specific contacts with the protein (and there was only a small energy difference between the crystal structures of systems F and I; see Table 1), and hence, docking was not as successful as with the truncated peptide Ace-Ala-Pro-Tyr (Fig. 1c). However, because the rigid ligand docks with 2 kcal/mole lower energy than the flexible one, and with low RMSD with respect to the crystal structure, we should conclude that the poor results with system I are owing to insufficient searching.
The Ace-Ala-Gly-Pro-NMe tripeptide (B) proved to be too small to perfectly mimic the binding loop of p24 protein (Fig. 3); a different conformation was found with lower energy than the crystal structure. In contrast, the Ace-His-Ala-Gly-Pro-Nme tetrapeptide was more successful (system G; see Fig. 1d): The subclass of the first class contained the conformer closest to the crystal structure, in two out of three jobs. The parameters of the first type of jobs (100 trials/10 × 106 energy evaluations) were not sufficient for finding the site of this larger peptide. The class/subclass populations were also lower than in the case of the above-mentioned shorter peptides: the minimization problem became more difficult. Ala-Leu-Ala-Leu is a simple peptide (system J; see Fig. 1e) but has the largest number of flexible torsions among our test systems. The docked conformers closest to the crystallographic one were reproducibly found in the first class and had the lowest energies in the second and third jobs, similarly to system G.