A Spanish Chemoinformatics GitBook for Chemical Data retrieval and Analysis using Python Programming
Authors:
- Fernanda I. Saldívar-GonzálezFernanda I. Saldívar-González
- Diana L. Prado-RomeroDiana L. Prado-Romero
- B. Raziel Cedillo-GonzálezBCB. Raziel Cedillo-González
- Ana L. Chávez-HernándezAna L. Chávez-Hernández
- Juan F. Avellaneda-TamayoJuan F. Avellaneda-Tamayo
- Alejandro Gómez-GarcíaAlejandro Gómez-García
- Luis Juárez-RiveraLuis Juárez-Rivera
- José L. Medina-FrancoJosé L. Medina-Franco
Preprint
- 12 January 2024
- preprint
- Published by American Chemical Society (ACS) in ChemRxiv
Abstract
Searching, retrieving, and analyzing chemical information is one of the main tasks faced by students and professionals in chemistry-related scientific disciplines. Currently, freely available modules developed in programming languages, such as Python, allow efficient data management and facilitate obtaining information and knowledge from the data. This manuscript describes an electronic handbook generated on the GitBook platform to introduce the Python programming language and the Analysis, computational representation, and visualization of chemical data. This manual explores the most common molecular representations of low molecular weight organic compounds and their applications in various contexts. It also illustrates the acquisition of chemical information from large public molecular databases such as ChEMBL and PubChem and the Analysis and visualization of chemical information using concepts such as chemical space. The GitBook is freely available and is expected to foster open science and facilitate learning for chemistry students at the undergraduate and graduate levels and professionals interested in chemical data analysis and visualization.Keywords
All Related Versions
- Version 1, 2024-01-12, ChemRxiv
- Published version: Journal of Chemical Education, 101 (6), 2549.
This publication has 21 references indexed in Scilit:
- Chemical Multiverse: An Expanded View of Chemical SpaceMolecular Informatics, 2022
- A Gentle Introduction to Machine Learning for Chemists: An Undergraduate Workshop Using Python Notebooks for Visualization, Data Processing, Analysis, and ModelingJournal of Chemical Education, 2021
- Informatics for Chemistry, Biology, and Biomedical SciencesJournal of Chemical Information and Modeling, 2020
- Teaching Cheminformatics through a Collaborative Intercollegiate Online Chemistry Course (OLCC)Journal of Chemical Education, 2020
- Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure–Activity Relationships through Web ApplicationsJournal of Chemical Education, 2020
- Convolutional Embedding of Attributed Molecular Graphs for Physical Property PredictionJournal of Chemical Information and Modeling, 2017
- SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small moleculesScientific Reports, 2017
- Chemoinformatics as a Theoretical Chemistry DisciplineMolecular Informatics, 2011
- Extended-Connectivity FingerprintsJournal of Chemical Information and Modeling, 2010
- Reoptimization of MDL Keys for Use in Drug DiscoveryJournal of Chemical Information and Computer Sciences, 2002