Thank you very much for this video!! My MSc thesis will be in drug design in silico and it helped me a lot. I have one question, at some point you type this command "from rdkit.Chem import PandasTools PandasTools.AddMoleculeColumnToFrame(data_small, smilesCol='SMILES_STD',molCol='ROMol')" and the output bellow the ROMol is the 3D structure. In my case when i run your code instead of the 3d structure i got this and not the molecule. Can you please guide me in order to have the 3D structures and not the other format? Thank you in advance!!
Hey man, I'm a Computer Science major working for a Chemistry professor and trying to use morgan fingerprints in rdkit for potential machine learning for coordination energies to do with Pd-PPh3. Because I'm a CS major I don't have a lot of prerequisite Chemistry knowledge to understand some of the information around morgan fingerprints. However, I know I want to build a machine learning model with the fingerprints developed from xtb optimized .mol files. I'm wondering if you have any resources to refer to or any advice. I'm a bit lost. I've been playing around with rdkit and getting morgan fingerprints from .mol files but not much else. Thanks!
Lots of good review articles in this space. For example, One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome link.springer.com/article/10.1186/s13321-020-00445-4;
I don't think I have ever seen a cbfv applied to organic molecules, but you could certainly give it a shot. The problem is that so many of these things are very limited variety of chemistry and large variety of structural motifs so it makes more sense to use things like smiles or fingerprints etc
Thanks for you videos I have listened every video . You are doing great job. I am also working on neural network
Neural net videos coming this week!!
great tutorial, thank you
Thank you so much for this tutorial
Thank you very much for this video!! My MSc thesis will be in drug design in silico and it helped me a lot. I have one question, at some point you type this command "from rdkit.Chem import PandasTools
PandasTools.AddMoleculeColumnToFrame(data_small, smilesCol='SMILES_STD',molCol='ROMol')" and the output bellow the ROMol is the 3D structure. In my case when i run your code instead of the 3d structure i got this and not the molecule. Can you please guide me in order to have the 3D structures and not the other format? Thank you in advance!!
Thank you so much for this
Super happy to help.
Hey man, I'm a Computer Science major working for a Chemistry professor and trying to use morgan fingerprints in rdkit for potential machine learning for coordination energies to do with Pd-PPh3. Because I'm a CS major I don't have a lot of prerequisite Chemistry knowledge to understand some of the information around morgan fingerprints. However, I know I want to build a machine learning model with the fingerprints developed from xtb optimized .mol files. I'm wondering if you have any resources to refer to or any advice. I'm a bit lost. I've been playing around with rdkit and getting morgan fingerprints from .mol files but not much else. Thanks!
Lots of good review articles in this space. For example, One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome link.springer.com/article/10.1186/s13321-020-00445-4;
@@TaylorSparks Thanks for quick response. Just found your instagram and realized we're both from Utah and ski tour. Cheers from Provo!
@@andrewhartsfieldii543 way rad. Lmk if you need more info or ever wanna hit a dawn patrol. 😎
thanks dude.
@Taylor Sparks Thanks for the tutorial! Just wondering if there is a link for the jupyter notebook you are using
On the course github github.com/sp8rks/MaterialsInformatics
@@TaylorSparks Great, thank you so much!
Can one use CBFV for organic molecules too? Or one should just stick to RDKIT, SMILE for organic molecules?
I don't think I have ever seen a cbfv applied to organic molecules, but you could certainly give it a shot. The problem is that so many of these things are very limited variety of chemistry and large variety of structural motifs so it makes more sense to use things like smiles or fingerprints etc