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Scores
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There were 7 questions found in this category:
 Are FlexX scores free energy values?
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 ...
- Are FlexX Units kJ/mol or kcal/mol
FlexX uses the units the Boehm LUDI paper works with; these are kJ/mol.However, for example, the max. achievable value of 4.7 kJ/mol per hydrogen bond is not the absolute value of the hydrogen bond energy (that would be a bit small) but instead, it corresponds to the contribution of the hydrogen ...
- Can I expect the same score values in FlexX, that I obtained in GOLD when I docked the same ligands in the same protein?
Actually, BioSolveIT does not currently have the GOLD score programmed into FlexX. The G-score is output by Tripos's CSCORE module, so we cannot guarantee that this answer is comprehensive. First off, according to TRIPOS, the G-score has been coded along the Jones/Willett et al paper (JMB 199 ...
- How can I use a different scoring function in LeadIT than the Boehm function?
In your installation directory, you will find a subfolder example/static_dataWe have prepared several geometry*dat files there which you can tell LeadIT to use.To this end, please:Go to the dialog LeadIT -> Global Preferences. Navigate to the Parameters&Flags tab (at the very right).Scroll t ...
- HowTo: Rescoring with FlexX
Start LeadIT in commandline mode: leadit --commandlineIt is of course possible to calculate a rescoring for a given complex. You can use the command SCORE that can be found in the menu DOCKING/ANALYZE. In this submenu you will also find further commands to analyze docking poses or given complex ...
- What is the meaning of the similarity index in FlexX
This similarity value has nothing to do with the FTrees similarity. It is very similar to the RMSD value given in the previous column. The RMS value however, is strictly restricted to calculate the RMSD between the 2 coordinates assigned to one atom: the docking solution coordinates and the ref ...
- Why is my score so strongly geometry dependent?
The reason for such score differences that you observe are due to an inherent problem of the FlexX scoring model rather than actually being a bug. Score differences of +/- 2 units are actually quite usual and if a hydrogen bond is not found (e.g. due to a different orientation of a hydrogen in t ...
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© BioSolveIT GmbH, 2012 |
Last modified Thursday, 09. Feb 2012 03:45 CET by WebMaster |
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