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FlexS
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There were 6 questions found in this category:
 Can FlexS accept a template molecule which is actually a collection of superimposed molecules?
This can be done with FlexS, but our solution is not working on multi-mol2 files for the following reason: Our superpositioning algorithm needs a connected molecule graph. At the moment we can't handle disconnected components, i.e. multiple, separate molecules. But what you can already do (sinc ...
- Can I change the individual scoring function terms?
The FlexS scoring function is derived from the Böhm empirical scoring function (H.J.Böhm, The development of a simple scoring function to estimate the binding constant for a protein-ligand complex of known three dimensional structure, JCAMD, 8 (1994), 243-256.). There is a short desc ...
- How do I select a base fragment?
It is now possible to run FlexS fully automatically for virtual screening purposes. We have adapted FlexS this task, so that it can be run in batch mode in order to process huge amounts of data. In contrast to the JMC paper, we have implemented a method to select the base fragment automatically ...
- WARNING: wrong left boundary detected.
This warning indicates that your input structure has an unusual geometry (e.g. from a rule based conformation generation). You should run an energy minimization on your structures, prior to working with them.
- What is RigFit? How does it relate to FlexS?
RigFit is a module within the FlexS-program. It allows rigid-body superpositioning of molecules and molecular fragments onto a reference molecule. The RigFit-method has been described in detail in C. Lemmen, C. Hiller, and T. LengauerRigFit: A new approach to superimpose ligand moleculesJournal ...
- What kind of preparation do the input compounds need?
Both, reference compound and test compound need to have partial charges and hydrogen atoms annotated. The test compound should also be in a reasonable low energy conformation since the bond lengths and angles are taken directly from the input structure. Deviations from standard angles may resul ...
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Last modified Saturday, 04. Feb 2012 11:45 CET by WebMaster |
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