Related Experiment Video
Updated: May 30, 2025
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
EFGs: A Complete and Accurate Implementation of Ertl's Functional Group Detection Algorithm in RDKit
1Biostatistics and Bioinformatics Unit, IMDEA Food, E28049 Madrid, Spain.
Abstract:
Functional groups are widely used in organic chemistry, because they provide a rationale to analyze physicochemical and reactivity properties. In medicinal chemistry, they are the basis for analyzing ligand-biomacromolecule interactions. Ertl's algorithm is an approach to extract functional groups in arbitrary organic molecules that does not depend on predefined libraries of functional groups. However, there is a lack of a complete and accurate implementation of Ertl's algorithm in the widely used RDKit cheminformatic toolkit. In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. For a RDKit molecule, it provides (i) a PNG binary string with an image of the molecule with color-highlighted functional groups; (ii) a list of sets of atom indices (idx), each set corresponding to a functional group; (iii) a list of pseudo-SMILES canonicalized strings for the full functional groups; and (iv) a list of RDKit labeled mol objects, one for each full functional group. The code is freely available in https://github.com/bbu-imdea/efgs and is part of the RDKit Contrib directory (https://github.com/rdkit/rdkit/tree/master/Contrib/efgs).
More Related Videos
11:44Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates
Published on: March 20, 2015
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Related Concept Videos
02:45Functional Groups
02:08Introduction to Functional Groups
Functional groups are group of atoms with specific chemical properties that occur within organic molecules and sometimes denoted as “R”. Functional groups are found along the carbon backbone of macromolecules can form chains or rings of carbon atoms. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of common functional groups
The table below summarizes some of the major functional...
02:22Overview of Advanced Functional Groups
Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
01:19Overview of Functional Groups
01:23Protecting Groups for Aldehydes and Ketones: Introduction
02:37Experimental Determination of Chemical Formula