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Published on: October 24, 2025
ProtChemSI: a network of protein-chemical structural interactions
Olga V Kalinina1, Oliver Wichmann, Gordana Apic
1Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
Nucleic Acids Research
|November 24, 2011
Summary
ProtChemSI expands the understanding of protein-small molecule interactions by collecting, annotating, and modeling complex structures. This database aids research in drug discovery and molecular biology.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Experimental determination of 3D protein-small molecule complex structures is rapidly increasing.
- Existing data is fragmented and requires comprehensive organization for broader accessibility.
Purpose of the Study:
- To create a comprehensive database of protein-small molecule complexes.
- To facilitate the study of molecular interactions through data collection, annotation, and predictive modeling.
Main Methods:
- Collected and annotated experimentally determined protein-small molecule complex structures.
- Developed models for potential complexes using protein and chemical structure similarity.
- Integrated data into the publicly accessible ProtChemSI database.
Main Results:
- The database contains 7,704 proteins from 1,803 organisms and 11,324 chemical compounds.
- It includes 202,289 complexes, with 178,974 being predicted structures.
- Provides a valuable resource for structural biology and drug discovery research.
Conclusions:
- ProtChemSI offers a unified and expanded resource for exploring protein-small molecule interactions.
- The database supports hypothesis generation and accelerates research in related fields.
- Public accessibility promotes collaborative advancements in understanding molecular mechanisms.
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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.
01:13Protein Organization
Overview