Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Chemical Symbols01:09

Chemical Symbols

A chemical symbol is an abbreviation that is used to indicate an element or an atom of an element. For example, the symbol for mercury is Hg. We use the same symbol to indicate one atom of mercury (microscopic domain) or to label a container of many atoms of the element mercury (macroscopic domain).
Some symbols are derived from the common name of the element; others are abbreviations of the name in another language. Most symbols have one or two letters, but three-letter symbols have been used...
Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
Introduction to Functional Groups02:08

Introduction 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 groups in organic chemistry. (The...
Molecular Compounds: Formulas and Nomenclature03:10

Molecular Compounds: Formulas and Nomenclature

Molecular compounds or covalent compounds result when atoms share electrons to form covalent bonds. Since there is no electron transfer, molecular compounds do not contain ions; instead, they consist of discrete, neutral molecules.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

How many protein pairs can we chemically target?

Drug discovery today·2026
Same author

ChemBang: Expanding the Chemical Space Around Small Molecules.

Molecular informatics·2026
Same author

SAFR: Enabling Fragment-Based Drug Discovery with a Synthetic Binding Pose Data Set.

Journal of chemical information and modeling·2026
Same author

Dissecting Polypharmacology in Phenotypic Screening to Resolve Ferroptotic and Necrotic Cell-Death Mechanisms.

ACS medicinal chemistry letters·2026
Same author

Sexual Dysfunctions Associated with Proton Pump Inhibitors: Insights from VigiBase, the World Health Organization Pharmacovigilance Database.

Drug safety·2025
Same author

Enhancing molecular property prediction through data integration and consistency assessment.

Journal of cheminformatics·2025

Related Experiment Video

Updated: Jun 1, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Indexing molecules with chemical graph identifiers.

Elisabet Gregori-Puigjané1, Rut Garriga-Sust, Jordi Mestres

  • 1Research Programme on Biomedical Informatics, IMIM-Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain.

Journal of Computational Chemistry
|June 8, 2011
PubMed
Summary
This summary is machine-generated.

A new chemical graph identifier (CGI) algorithm improves molecule indexing by correcting errors and handling complex isomerism. This enhanced molecular indexing is crucial for managing large chemical libraries and identifying duplicates accurately.

More Related Videos

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Related Experiment Videos

Last Updated: Jun 1, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Data science

Background:

  • Effective molecular indexing is vital for managing large chemical libraries.
  • Existing algorithms like the Morgan algorithm have limitations, including collisions and difficulties with complex chemical structures.
  • Accurate compound uniqueness definition is critical for library management tasks like duplicate analysis.

Purpose of the Study:

  • To introduce a modified and extended molecular equivalence number naming adaptation of the Morgan algorithm.
  • To develop a robust chemical graph identifier (CGI) that addresses limitations of previous methods.
  • To validate the CGI's performance on large, diverse chemical databases.

Main Methods:

  • Modification and extension of the Morgan algorithm for molecular equivalence number naming.
  • Implementation of a new chemical graph identifier (CGI) addressing collisions and isomerism.
  • Validation using the NCI database (260,071 structures) and the ZINC database (5,348,089 structures).
  • Comparison of CGI performance against CACTVS hash code and InChIKey.

Main Results:

  • The modified algorithm successfully corrects collisions found in the original Morgan adaptation.
  • The CGI effectively handles graph canonicalization, ensembles (salts), and various forms of isomerism (tautomerism, regioisomerism, optical, geometrical).
  • Validation on large databases demonstrates the CGI's robustness and accuracy.

Conclusions:

  • The developed CGI offers a flexible and accurate method for molecular indexing.
  • This improved indexing impacts compound management, particularly in duplicate analysis of chemical libraries.
  • The choice of molecular index influences the sensitivity of compound uniqueness definitions, though the impact is minor.