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FlexX is tested on an increasing set of receptor-ligand complexes with known three-dimensional structures taken from the Protein Data Bank. The run time needed for the prediction of a receptor-ligand complex is about 2-3 minutes on a current day workstation.
Complexes we have considered so far and the predictions achieved with
FlexX are listed in the following table (see also
[RKL96]). Three-dimensional structures of the
predicted receptor-ligand complexes are presented as VRML files
(You can activate your VRML-Browser in the way described on our
help-page.).
The color-coding for these graphics is :
| green | amino acids of the receptor interacting with the ligand |
| red | for the position of the ligand in the X-ray structure |
| yellow | predicted position of the ligand |
| dashed | interactions between the ligand and the receptor in the predicted position. The color indicates the strength of the interaction (red (strong) -- yellow (medium) -- blue (weak)). |
| PDB-Code | runtime | highest rank | best prediction | exp.energy | |||||
|---|---|---|---|---|---|---|---|---|---|
| rms | energy | VRML | rank | rms | energy | VRML | |||
| 5tim | 0:03 | 1.99 | -12.7 |  |
3 | 0.87 | -10.3 | |
-13.1 |
| 1ldm | 0:11 | 0.62 | -32.8 | |
1 | 0.62 | -32.8 | |
-30.8 |
| 2phh | 0:36 | 0.58 | -25.6 | |
1 | 0.58 | -25.6 | |
-26.7 |
| 3ptb | 0:18 | 0.48 | -28.3 | |
1 | 0.48 | -28.3 | |
-27.2 |
| 1ulb | 0:46 | 0.65 | -17.9 | |
1 | 0.65 | -17.9 | |
-30.2 |
| 3tpi | 0:34 | 0.58 | -24.0 | |
1 | 0.58 | -24.0 | |
-24.5 |
| 4ts1 | 0:13 | 2.01 | -16.1 | |
15 | 0.71 | -11.8 | |
-32.0 |
| 4dfr | 0:81 | 1.38 | -67.0 | |
2 | 0.90 | -65.3 | |
-55.3 |
| 1stp | 0:24 | 0.81 | -31.2 | |
1 | 0.81 | -31.2 | |
-76.4 |
| 1dwd | 1:46 | 2.12 | -42.6 | |
23 | 0.63 | -38.6 | |
-48.6 |
| 1dwc | 1:44 | 2.66 | -32.0 | |
13 | 1.20 | -29.1 | |
-44.0 |
| 6rsa | 0:46 | 0.85 | -35.9 | |
1 | 0.85 | -35.9 | |
-28.5 |
| 1rnt | 0:73 | 1.48 | -42.0 | |
47 | 0.96 | -31.4 | |
? |
| 1tmn | 1:47 | 0.87 | -39.1 | |
1 | 0.87 | -39.1 | |
-41.6 |
| 4tln | 0:03 | 4.50 | -15.8 | |
106 | 0.93 | -8.6 | |
-21.2 |
| 3cpa | 0:90 | 3.08 | -35.3 | |
3 | 1.06 | -32.9 | |
-22.1 |
| 2ctc | 1:07 | 0.65 | -30.3 | |
1 | 0.65 | -30.3 | |
-22.2 |
| 4phv | 1:31 | 1.04 | -38.2 | |
1 | 1.04 | -38.2 | |
-52.2 |
| 121p | 0:81 | 2.00 | -50.0 | |
43 | 1.14 | -30.5 | |
? |
(runtime in minutes:seconds on a SUN UltraSPARC Workstation; rms given in A, energy given in kJ/mol)
(21. August 1996)
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