Related Experiment Video
Updated: May 12, 2026
05:34
Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
Published on: June 6, 2025
Extracting and connecting chemical structures from text sources using chemicalize.org.
Christopher Southan1, Andras Stracz
1TW2Informatics Ltd, Göteborg, 42166, Sweden. cdsouthan@hotmail.com.
Journal of Cheminformatics
|April 27, 2013
Summary
Chemicalize.org enhances bioactive chemistry exploration by linking structures across documents and databases like PubChem. This tool aids in discovering chemical information and connections, advancing medicinal and chemical biology research.
Area of Science:
- Bioactive chemistry
- Medicinal chemistry
- Chemical biology
Background:
- Navigating chemical structures and data from diverse text sources is challenging.
- PubChem has millions of document-extracted structures, but inter-document links are limited, especially for journal articles.
- chemicalize.org expands access to chemical information embedded in text.
Purpose of the Study:
- To explore the utility of chemicalize.org for connecting chemical structures within documents and to databases.
- To demonstrate how chemicalize.org facilitates answering questions about chemical structures and their database overlaps.
- To illustrate these capabilities using Dipeptidyl Peptidase 4 (DPPIV) inhibitors as a case study.
Main Methods:
- Utilized chemicalize.org to process IUPAC names, SMILES, and other identifiers from various text formats (PDFs, URLs).
- Extracted chemical structures and properties, launching searches in databases like PubChem.
- Performed set intersections to identify common compounds between documents and merged extractions.
Main Results:
- Successfully downloaded over 1400 DPPIV inhibitor structures from a patent and aligned them with IC50 data.
- Uploading SMILES to PubChem revealed extensive linking to patents and publications.
- Extracted over 500 DPPIV inhibitor structures from PubMed abstracts, linking them to PubChem and identifying previously unlinked IUPAC names.
Conclusions:
- chemicalize.org effectively demonstrates chemical structure connectivity between documents and databases.
- The tool integrates with other open resources and is under continuous development.
- This facilitates advancements in medicinal chemistry, chemical biology, and other bioactive chemistry fields.
Related Concept Videos
02:00Molecular 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.
03:05Acid Strength and Molecular Structure
Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
02:34Molecular Structure and Acidity
An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:28Structures of Carboxylic Acid Derivatives
Structure of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
02:40Chemical Bonds
Atoms participate in a chemical bond formation to acquire a completed valence-shell electron configuration similar to that of the noble gas nearest to it in atomic number. Ionic, covalent, and metallic bonds are some of the important types of chemical bonds. Bond energy and bond length determine the strength of a chemical bond.
Types of Chemical Bonds
An ionic bond is formed due to electrostatic attraction between cations and anions. Often, the ions are formed by the transfer of electrons from...