9 Matching Annotations
- Oct 2020
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rdkit.blogspot.com rdkit.blogspot.com
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From the molecules in the candidate pool find the one that has the maximum value for its minimum distance to molecules in the picked set (hence the MaxMin name), calculating and recording the distances as required. This molecule is the most distant one to those already picked so is transferred to the picked set.
a good summary of MaxMin method
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- May 2020
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ositionalCartesian restraint
Cartesian restraints are available in Schrodinger MacroModel, how to implement them? some example scripts are included in Additional file 1 of this article
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relax ligand-receptor complexeswithout causing major alterations of their originalgeometry, or to perform a torsional scan on a selecteddihedral while relaxing the rest of the molecule.
such functions are like Schrodinger MacroModel, how to implement them?
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- Apr 2020
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- Mar 2020
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better O3A alignments give higher scores
O3A alignment conformation generation, need to add Hs and use MMFF force field
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asteeves.github.io asteeves.github.io
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GetDihedralConfDegree
rdkit can measure dihedral. How to define the dihedral? seems user needs to provide 4 atom ids, but how to get the ids? Method 1. Use PyMOL to load the structure, and show label>Atom properties>Rank. Then the atom id will be labelled Method 2. Use SMARTS? How to?
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www.rdkit.org www.rdkit.org
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legendFontSize
this can control the label size
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www.samson-connect.net www.samson-connect.net
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this tool seems like DataWarrior, and it uses RDkit
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