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. Author manuscript; available in PMC: 2013 Oct 22.
Published in final edited form as: J Chem Inf Model. 2012 Sep 17;52(10):2705–2714. doi: 10.1021/ci3001088

Table 3.

Summary of the results before and after ALiBERO optimization of a homology model of the A2A adenosine receptor in complex with the ligand ZM24138. The RMSD of the ligand (with and without the very flexible phenoxy-ring) was performed after receptor superimposition to the PDB ID 3EML. The coverage of contacts was defined as the number of equivalent ligand-receptor atomic contacts between the reference and the target, divided by the contacts in the reference (4 Å cutoff used).44

Raw Homology Model
Training Set AUC NSQ_AUC Ligand RMSD (Å) Contacts Coverage ICM Docking Score
Tr1:1 0.63 0.29 7.5 / 7.4 21% −17.9 (kcal/mol)
Tr1:15 0.66 0.26 ~ ~ ~
ALiBERO
Training Set AUC NSQ_AUC Ligand RMSD (Å) Contacts Coverage ICM Docking Score
Tr1:1 0.96 0.92 6.2 / 4.3 47% −28.7 (kcal/mol)
Tr1:15 0.92 0.78 4.6 / 2.8 51% −28.8 (kcal/mol)