Data Warrior - patrickchirdon/AIdrugdiscovery GitHub Wiki
http://www.openmolecules.org/datawarrior/
This is a really useful tool to generate a chemical library very quickly based on a scaffold.
Click Chemistry --> create an evolutionary library --> select druglike
Then you can edit each of the molecules by hand so that they conform to your criteria. Be sure to obtain the SMILES for each. However, please note that when you create a new chemical library using SMILES, you will need to use the --gen3D option of open babel to get 3D coordinates if you want to do docking with Rosetta.
Data Warrior--
http://www.openmolecules.org/help/chemistry.html#EvolutionaryLibraries
Evolutionary library-
mutation algorithm- single atom replacements, atom insertions, bond order changes, aromatization
mutations that improve druglikeness are gien a higher probability
mutations that create ring strain are removed
-each generation is checked for fitness, best structures serve as starting point for next generation
Our fitness algorithm was paramaterized so that they have similar flexophores, similar target binding behavior and with similar chemical structure.
Activity cliff analysis--
randomly position all molecules on the 2D space.
- calculate the entire similarity matrix between all values
-locate most similar neighbors to be considered for every molecule
-between any 2 neighbors assume attractive forces, which increase with similarity and distance
-stepwise relocate all molecules parallel to the mean vector of perceived forces
-while attractive forces decrease over time and due to lower distances, introduce short range repelling forces among all molecules
-Similar neighbors are connected with a connecting line and markers that represent the molecules are colored dynamically by molecule similarity to the chosen current molecule, which changes whenever you click on another molecule
SALI plot-- my graph shows the SALI plot for ligand efficiency. The higher the SALI index, a smaller change in chemical structure can result in a larger change in chemical activity, in this case we've selected ligand efficiency.