This is a continuation of a 2 part series in predicting the products of a chemical reaction using deep learning methods. Checkout the first part here. In part 1, we: First introduced the problem statement Then we saw how a molecule is represented in a graph network| ChemicBook
Reactant A and B reacts to form the products C and D. The chances are that you have encountered this type of chemical reaction in your school days. While on paper they may seem as simple as drawing a bunch of arrows, in the real world, even the simplest of those reactions, takes a long time, money, and resources to formulate. The reaction time can vary from the order of seconds to the order of months.| ChemicBook
Extended-Connectivity Fingerprints(ECFPs) are a type of molecular fingerprint explicitly designed to capture molecular features relevant to molecular activity. They are among the most popular similarity search tools in drug discovery and they are effectively used in a wide variety of applications.| ChemicBook
Unless you’re living under a rock, you probably have heard about ChatGPT by now. The Internet has been buzzing with new technologies for the past few months. Tools that would have taken months, possibly years, to build are being developed just over a weekend of hacking. I truly believe that we’re living in one of the most exciting times in history.| ChemicBook
Let’s try to get a brief overview of what UMLS is, and then we’ll jump into more details. So, in simple terms, UMLS is a collection of many controlled biomedical vocabularies to provide cross-walk among them and to enable interaction between computer systems. To simplify it further, there are multiple biomedical vocabularies out there developed by different organizations. Each of them has come up with their own set of IDs assigned to each term. UMLS helps in mapping each of them to one co...| ChemicBook
Introduction The advances in Machine Learning field have proven useful ranging from applications in Natural Language Processing to Computer Vision. These remarkably successful demonstrations have drawn high interests from the physical and biological science communities.| ChemicBook
In RdKit, the method SetProp is used to set an atomic property for the atoms involved in the molecule. This method takes two arguments: the peroperty to set and its value. The idea is simple: Create an rdkit mol object from SMILES string, iterate over the atoms, and set the desired property to a custom value.| ChemicBook
Welcome to the second blog in the Cheminformatics for Beginners series. In the last blog, we saw a quick introduction to the SMILES notation. This post will introduce you to the mol2 format in cheminformatics. Introduction One major setback from the SMILES notation was that it could not provide the positions of each atom in space, typically with X, Y, and Z cartesian coordinates. Mol2 file solves this problem. It is a plain text tabular format that represents a single or multiple chemical com...| ChemicBook
Welcome to the first article in the Cheminformatics for Beginners series. This blog will introduce you to the SMILES string notation in cheminformatics. Introduction SMILES (Simplified molecular-input line-entry system) is a line notation method to represent molecules as well as reactions. It is one of the most common method to represent molecules because of its simplicity and readability to the human eye.| ChemicBook