Skip to main content

Advertisement

Table 2 Fraction (%) of ligands similar to the reference crystal pose depending on charge and solvent

From: Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?

Force field Charged (I) Neutralized (II) Combined (III)
<0.5 Å <1.0 Å <0.5 Å <1.0 Å <0.5 Å <1.0 Å
OPLS2005-chloroform 38.6 68.4 43.5 77.1 47.3 79.9
OPLS2005-octanol 40.8 71.1 45.0 77.5 48.9 80.1
OPLS2005-water 39.9 76.9 47.1 82.2 49.6 84.7
MMFFs-chloroform 35.8 67.6 43.4 74.4 46.1 77.9
MMFFs-octanol 40.4 71.1 45.1 79.1 48.2 82.3
MMFFs-water 40.9 77.4 47.3 81.7 50.2 84.3
AMBER-chloroform 36.7 67.5 43.0 75.0 46.2 77.8
AMBER-octanol 38.3 69.2 44.7 76.0 46.6 78.2
AMBER-water 43.1 77.4 45.5 79.0 48.6 81.3
OPLS3-chloroform 39.6 69.3 46.8 74.2 49.9 79.0
OPLS3-octanol 43.8 74.4 50.2 79.0 53.4 82.1
OPLS3-water 47.8 81.6 53.5 81.7 57.4 86.8
  1. Conformer RMSDs were calculated taking crystal pose as reference for; (I) conformational search performed with charged input structures, (II) conformational search performed with neutralized input structures, (III) combined pool of (I) and (II)