Skip to main content

Table 1 Results of five-fold leave-one-out cross-validation.

From: Predicting protein ligand binding motions with the conformation explorer

     sRMSD (Å)  
Protein apo
PDB
holo
PDB
ligand starting lowest in ensemble predicted holo server ID
RBP 1URP 1DRI ribose 12.1 7.0 14.8 ce828024-27360
ADK 2AK3 1AK2 SO4 17.0 3.8 11.2 ce829841-12334
RBP 1URP 1DRI ATP 12.1 3.5 5.8 ce105518-17825
ADK 2AK3 1AK2 ATP 17.0 4.6 5.3 ce131413-8235
GlnBP 1GGG 1WDN glutamine 15.7 4.2 5.3 ce963091-2997
BC 1ULZ 1DV2 ATP 14.8 6.7 10.9 ce889203-5498
MurA 1EJD 1A2N T6361 4.9 4.8 9.0 ce336773-19756
  1. The five proteins (RBP, ADK, GlnBP, BC, and MurA) were each submitted to CE. For each protein, the parameters of f were fitted using the results of the other four proteins. In a preliminary round we computed closure of RBP binding its natural ligand, ribose, and of ADK binding SO4 (with which it has been cocrystallized in holo form) but sRMSD of the predicted structures was high (14.8 and 11.2Å, italic type). In the final round of calculations these two proteins were submitted with ATP as a ligand (next two rows, regular type), resulting in much lower sRMSD. GlnBP and BC were submitted with their natural ligands, and MurA with an antibiotic.