There shouldn't be any expectation that the MMFF energy should converge to
1kcal/mol.
There *may* be a case to be made for the MMFF_energy - Global_minimum be <
1kcal/mol, however, in general, we don't know what the global minimum is.
I suggest looking at this paper:
The code below shows the lowest energy found for 6 different protomers defined
by the smiles strings below as a function of number of conformers. Even with
2000 conformers I am not getting convergence to within 1 kcal/mol for
comp109_1=2.
Is this expected? Any advice or tips appreciated
" A clustering algorithm, that does not require specifying the number
of classes upfront (so not K-means)."
A general approach to O(N) hierarchical clustering is:
1. Pick a random sqrt(N) structures.
2. Do full hierarchical O(N^2) clustering on these.
3. Select your favored clustering level to
Hi,
Thanks for all the answers, especially those pointing to code
examples, very useful.
I should be more specific when asking about clustering >2M compounds.
An example I would like to see would use:
1. A clustering algorithm, that does not require specifying the number
of classes upfront (so
Hi Fabrice,
We usually don't finalize the program until very close to the meeting
itself; usually a week or so before the meeting starts.
The best way to get an idea for the type of content is to look at the
programs from previous years:
https://github.com/rdkit/UGM_2016/blob/master/Agenda.pdf
Hi all,
Could you give us more detail about the UGM 2017 in Berlin?
For example details about schedules of each day ?
Sincerly
Fabrice
Fabrice Carles - PhD student
Structural Bioinformatics & Chemoinformatics,
Institut de Chimie Organique et Analytique (ICOA)
University of Orleans - France
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