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Category Icon Charges (2)
Category Icon Scores (7)
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There were 11 questions found in this category:
  1. questionAre 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 ...

  2. questionCan 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 ...

  3. questionDelocalisation 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 ...

  4. questionHow can I use a different scoring function than the Boehm function?
    Release 3:Go to the dialog File | Global Preferences. Adjust the settings as described below in the respective editor for the static-data entries mentioned in the following for Release 2.The changes in config.dat are obsolete with Release 3. In the future, we will be supporting switching betwee ...

  5. questionHow 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 ...

  6. questionHowTo: Add a metal ion to the RDF
    Release 3.1 (pre) and newer:Metals and respecting their coordination chemistry are supported in the GUI intuitively during the receptor preparation. RDF handling is obsolete.Release 2, 3.0 and older:In order to add metal ions to the Receptor Description File (RDF) you have to add two lines to t ...

  7. questionHowTo: 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 ...

  8. questionHowTo: The Protonation of protein amino acids
    Release 3 and newer: The GUI's wizard (Receptor | Define) will guide you through the necessary steps. Release 2 and older: Using the RDF file On the receptor side, the protonation is controlled by the RDF-file which contains information about the protein and the residues that define the binding ...

  9. questionHowTo: Use a Gaussian Filter
    Release 3:* Use the access_scaling dialog in DOCKING | DEFINE | SCORING.* For more advanced configuration, start FlexX/-SIS using the commandline (flexx --cli), then proceed as below. Release 2: Preconception: FlexX placements are sometimes found at the rim of the binding site. True — b ...

  10. questionWhat 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 ...

  11. questionWhy 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 ...

Last modified Wednesday, 08. Sep 2010 15:45 CEST by WebMaster