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

From: Predicting protein ligand binding motions with the conformation explorer

    

sRMSD (Ã…)

 

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 11.2Ã…, 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.