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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.
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Chemistry of the Cell02:58

Chemistry of the Cell

The cell is chemically composed of water, organic molecules and inorganic ions.
Water
The polarity of the water molecule and its resulting hydrogen bonding makes water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in an aqueous environment, and most of an organism’s cellular chemistry and metabolism occur inside the aqueous contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of...
Chemistry of the Cell02:58

Chemistry of the Cell

The cell is chemically composed of water, organic molecules and inorganic ions.
Water
The polarity of the water molecule and its resulting hydrogen bonding makes water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in an aqueous environment, and most of an organism’s cellular chemistry and metabolism occur inside the aqueous contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...

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Related Experiment Video

Updated: May 29, 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

PubChem3D: a new resource for scientists.

Evan E Bolton1, Jie Chen, Sunghwan Kim

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov.

Journal of Cheminformatics
|September 22, 2011
PubMed
Summary
This summary is machine-generated.

PubChem3D enhances PubChem by adding a 3D layer for analyzing chemical structures and their biological activities. This new resource aids in discovering relationships not apparent with traditional 2D similarity methods.

Related Experiment Videos

Last Updated: May 29, 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

Area of Science:

  • Chemical informatics
  • Structural biology
  • Drug discovery

Background:

  • PubChem is a public repository for small molecules and their biological activities.
  • Traditional 2D similarity methods struggle to interrelate diverse chemical structures with similar biological efficacies.
  • A new 3D layer, PubChem3D, is introduced to address these limitations.

Purpose of the Study:

  • To enhance PubChem by incorporating 3D structural information.
  • To enable the analysis of chemical structures based on their 3D conformations.
  • To facilitate the discovery of novel structure-activity relationships.

Main Methods:

  • Generation of 3D conformer models for over 92% of PubChem Compound records.
  • Redundancy sampling of conformer models to ensure diversity.
  • Pre-computed 3D similarity searches for immediate access to related compounds.

Main Results:

  • PubChem3D provides comprehensive 3D conformer descriptions for a vast number of chemical records.
  • 3D similarity searches reveal connections between chemical structures and biological functions missed by 2D methods.
  • New capabilities for searching, visualizing, and analyzing chemical data in 3D are now available.

Conclusions:

  • PubChem3D significantly expands PubChem's utility by adding a crucial 3D dimension.
  • This resource allows for the uncovering of latent structure-activity relationships.
  • PubChem3D complements existing 2D analysis, offering a powerful new tool for scientific exploration.