We are a group of Master's degree students, majoring in Microbiology. We were introduced to Computational biology and were very interested in the subject. We decided to do a project on the QSAR analysis of drug molecules.
But we hit a wall and are unable to proceed further after the collection of Molecular descriptors and molecule Activities( Pc50/ Ec50).
We have read many papers, but are still confused as to what to do.
Can anyone please guide us with a workflow on how to do 2D QSAR analysis?
You may refer to the following tutorial videos:
1) How to do QSAR : Live Demo on PaDEL and QSARINS (https://www.youtube.com/watch?v=G9dvzzLTE60)
2) 1D/2D QSAR model building; AutoQSAR (https://www.youtube.com/watch?v=Du4h9voRcvk)
3) QSAR (Quantitative Structure Activity Relationship) Analysis Practical Session (https://www.youtube.com/watch?v=20gu49AIga0&t=2079s)
You need 2D descriptors for doing 2D QSAR. Chemicals that are active against a certain target (training set) needs their corresponding biological activities (IC50, EC50, Kd, ...). Furthermore, you need to validate your model based on some inactive decoys or a set of inactive chemicals as a test set.
This might help:
https://www.youtube.com/watch?v=BX80RYr1f08
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