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Updated: Jul 19, 2026
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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
Published on: April 1, 2017
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.
Petras J Kundrotas1, Emil Alexov
1Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
Nucleic Acids Research
|October 31, 2006
Summary
The Protein Complexes (PROTCOM) database offers 3D structures of protein-protein interactions, including artificial domain-domain structures. It serves as a valuable resource for benchmarking prediction algorithms and modeling protein complex structures.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein-protein interactions are crucial for cellular functions.
- Understanding the 3D structures of protein complexes is essential for deciphering biological mechanisms.
- Existing databases may lack comprehensive collections of protein complex structures and related domain information.
Purpose of the Study:
- To introduce the Protein Complexes (PROTCOM) database, a curated collection of 3D protein complex structures.
- To provide artificially generated domain-domain structures to enhance the utility of the database.
- To offer a platform for benchmarking protein structure prediction algorithms and homology modeling.
Main Methods:
- Compilation of known 3D structures of protein complexes from the Protein Data Bank.
- Generation of artificial domain-domain structures by parsing single chain protein structures.
- Development of an integrated set of tools for database access, including browsing, searching, visualization, and downloading.
- Implementation of a multi-criteria search functionality (up to 10 criteria).
Main Results:
- The PROTCOM database contains 1770 entries as of July 2006.
- Each entry includes known 3D structures and relevant associated information.
- Data can be accessed in both text-only and visual modes.
- The database incorporates unique artificial domain-domain structures.
Conclusions:
- PROTCOM serves as a valuable resource for researchers in structural biology and bioinformatics.
- The database facilitates the benchmarking of docking and structure prediction algorithms.
- PROTCOM can be utilized as a template database for homology and threading-based modeling of protein complexes.
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