Research Article

Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

Table 2

IN/INN values for all tested 16 protein-ligand complexes and all 7 minima sets. “inf” for IN means that all (1024 minima) calculated low-energy minima have energy below the energy of the optimized native ligand. “inf” for INN means that all the low-energy minima found by FLM have RMSD from the native position above 2 Å.

PDB IDMMFF94MMFF94 + PCMPM7PM7 + COSMOMMFF94MMFF94 + PCMMMFF94 + SGB

4FT036/208/737/121/1180/99164/1598/6
4FT945/281/125/61/1194/1253/11/1
4FSW5/56/640/4012/13110/102134/14021/3
4FTAinf/inf4/inf379/inf1/infinf/inf186/18797/97
4FV5204/1313/3253/1942/1186/1346/35/5
4FV6inf/inf1/inf49/inf1/inf86/2893/681/24
1DWCinf/670245/25689/661158/141245/114250/35107/8
1TOMinf/inf13/infinf/inf1/infinf/inf13/47/1
1C5Y1/12/17/12/11/12/11/1
1F5L1/11/143/1669/301/110/11/1
1O3P20/1821/15/13/169/62274/1130/2
1SQO1/12/11/11/11/154/15/1
1VJ946/186/5132/126/86/111/1810/14
1VJA42/37/17/46/44/491/21/1
2P9436/219/123/67/122/135/121/1
3CEN96/118/113/13/190/135/113/1