Take a set of molecules (possibly each other similar, they should be an homogeneous series, like aromatic amines..) describe these molecules by chemico-physsical descriptors (logP, MR, MW, HOMO, LUMO..) or molecular formulas fingerprints so to have a bunch of X variables to use for predicting an observed Y variable (biological activity), build a model by principal componetn regression, multiple regression, linear discriminant analysis or whatsoever you want and predict the maximal activity expected on the basis of the model, synthetize the molecule predicted to be active and check if you was right, this is computer aided drug design, once known as QSAR (Quantitative Structure Activity Relationships) since 1964 pioneering Hansch work, I suggest you to read the beautigul Rainer Franke book about 'Theoretical Drug Desing Methods' it is still the best...

First of all, you have to know which properties you want to study. In your molecules, which ones are more important? LogP, MR, MW? First of all, find a common propertie that correlates well with your molecules. From there, check other related propeties and then distinct properties. You can make a Hansch analysis as already referred, but if you have activity and the protein receptor, you can also make docking or 3D-QSAR.

I advice you yo read chapter 11 and chapter 13 in "An Introduction to Medicinal Chemistry by Graham Patrick, 2nd edn (2002)". These two chapters will be a very easy introduction to CADD.

Hello Friend "Computer Aided Drug Design" is a broad field --- in a very simple term here you perform and study the interaction between a drug like molecule or a chemical entity to a biological molecule it can be either a protein, DNA or both. CADD has a number of steps and each of them are extensive broad field example: Molecular Sketching, Docking studies, SAR and QSAR.

you can simply refer wikipedia and

Abdualrahman M. Abdualkader has referred a appropriate chapters.

if any doubt you can ask me any time:

[email protected] - 9323250900

Not all applications of computational chemistry to drug discovery are CADD, so the title of your question was confusing. What you want seems to be some simple descriptor calculations : polar surface area or fractional polar surface area. They can be obtained from most cheminformatics software, some available freely for on-line use. A number of software are available for calculating pKa, mostly commercial. Google!

Hello

Computer-aided drug design (CADD) techniques are used for the rapid assessment of chemical libraries in order to guide and speed up the early-stage development of new active compounds.

Check in these links. It might help you.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5248982/

http://file.scirp.org/Html/5-1790023_26238.htm

Books

Computer-Aided Drug Design and Delivery Systems

Book by Ahindra Nag and Baishakhi Dey

Computational drug design

Book by David C. Young

The Organic Chemistry of Drug Design and Drug Action

Book by Richard Bruce Silverman