|
|
 |
|
Welcome to our knowledge base. To find what you're after, use the search box below or choose a category to view listed questions.
|
 Search the Knowledgebase |
|
 Browse by Category |
|
|
|
|
|
|
|
| Are FlexX scores free energy values? |
| User Opinions |
100%
0%
(9 votes)
|
|
Thank you for rating this answer.
|
Although given in kJ, the scores predicted by FlexX are not free energy values. In the best case they are only very rough approximations. The scoring is used for distinguishing good from bad placements and not for predicting binding affinities. So, we advice you to not use the scores in this way.
If you think you have a much better scoring function please let us know and we will try to have it built in.
|
| Visitor Comments |
-
Comment #1 (Posted by Anonymous)
If it is very rough approximations, why then it is important to underline unit as kJ/mol?
* biosolveit answers:
The unit lies in the history of the derivation of the FlexX score. Most of the original values were taken from experimentally observed data in LUDI.
and if the scores are not related with free energy, why it is mentioned:
"A detailed analysis of binding modes generated by FlexX for a test set of 200 examples suggests that in about 80% of the cases a binding geometry close to the native pose is generated among the multiple solutions" at J. Mol. Biol. 295, 337-356, 2000 by Klebe et al.
* biosolveit answers:
FlexX produces not just one but usually many poses. Generating such poses and ranking them are two faces of a coin. The above mentioned quote refer to the pure generation of the respective poses - which is decoupled from a final scoring producing the ranking. To correlate binding affinities with scores, one would typically take the rank no.1 pose.
|
| Related Questions |
|
No related questions were found.
|
| Attachments |
|
No attachments were found.
|
|
|
© BioSolveIT GmbH, 2012 |
Last modified Thursday, 09. Feb 2012 04:45 CET by WebMaster |
|
Print this page
Email this page
Post a comment
Subscribe me
Add to favorites