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Chemical Issues
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There were 8 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 ...
- 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 ...
- Delocalisation of formal charges
Release 3 In Release 3, you can edit how ligands are initialized using the Ligands&Libraries dialog. After loading an input file, there is an icon which looks like a pencil. Click this to modify all initialization including the charges.At the commandline (flexx --commandline) you can still acc ...
- 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 ...
- How to force amides to be treated as planar?
If you feel that amides in your particular application should be treated as planar, you can force them to be so by adjusting the corresponding section in the static data file torsion.dat. 1. First you need to decrypt the file torsion.dat which is done in FlexX in the menu DATABASE/DECRYPT. Fo ...
- HowTo: Covalent Docking
Release 3:Start FlexX/-SIS in commandline mode(flexx --commandline); then proceed as described below.Release 2 and older:Many people don't even know that FlexX can dock covalently bound ligands. Therefore, we found it all the more important to bring this topic to our readers' attention. In the ...
- 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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