What Is Molecule Structure

This section provides a quick introduction on what is atomic bond that ties atoms together to form molecules.

What Is Molecule Structure? Molecule Structure is a graphical model of a molecule on how its atoms are bonded together, with information about atom types/sizes/locations and bound types.

Molecule Structures are 3-dimensional structures which can be visualized in different models. Two examples are list below:

Skeletal Formula - Also called line-angle formula or shorthand formula. Skeletal Formula uses line segments to represent atomic bonds, intersections/ends of line segments to represent atoms, and element symbols to identify atom types. For example, the picture below shows a Skeletal Formula of the Methane molecule:

Methane Molecule in Skeletal Formula
Methane Molecule in Skeletal Formula

Ball-and-Stick Model - Ball-and-Stick Model uses balls to represent atoms, sticks to represent bonds, and colors to identify atom types. For example, the picture below shows a Ball-and-Stick Model of the Methane molecule:

Methane Molecule in Ball-and-Stick Model
Methane Molecule in Ball-and-Stick Model

Table of Contents

 About This Book

Introduction of Molecules

 What Is Molecule

 What Is Molecular Formula

 What Is Atomic Bond

What Is Molecule Structure

 Skeletal Formula Notations

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB