https://sinembudak.com/tags/smiles/Recent content in SMILES on Sinem's BlogHugo -- gohugo.ioen-us© 2026. Sinem Demirkaya-BudakMon, 06 Apr 2026 16:00:06 +0300https://sinembudak.com/posts/smiles-a-universal-language-for-molecular-structures/Mon, 06 Apr 2026 16:00:06 +0300https://sinembudak.com/posts/smiles-a-universal-language-for-molecular-structures/SMILES stands for Simplified Molecular Input Line Entry System. It’s a notation for describing molecular structures using ASCII strings. Instead of drawing complex 2D or 3D molecular diagrams, SMILES represents molecules as simple text sequences that capture all essential chemical information. For example: Methane (CH₄): C Ethanol (C₂H₅OH): CCO Benzene (C₆H₆): c1ccccc1 Aspirin (acetylsalicylic acid): CC(=O)Oc1ccccc1C(=O)O How SMILES Works SMILES uses a set of simple rules to encode molecular information:https://sinembudak.com/posts/understanding-morgan-fingerprints/Sat, 07 Mar 2026 01:52:30 +0300https://sinembudak.com/posts/understanding-morgan-fingerprints/When I started learning cheminformatics, I struggled with a basic question: how do computers compare molecules? Then I discovered Morgan Fingerprints, and it all made sense. The Problem You can’t store entire molecular structures in a database and compare millions of them — it’s too slow. You need a compact representation that captures what makes a molecule unique. What Are Morgan Fingerprints? A Morgan Fingerprint converts a molecule into a binary vector — a string of 1s and 0s.