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Update of KDBI: Kinetic Data of Bio-molecular Interaction database
1Bioinformatics and Drug Design Group, Centre for Computational Science and Engineering, National University of Singapore, Blk S16, Level 8, 3 Science Drive 2, Singapore 117543.
Nucleic Acids Research
|October 31, 2008
Summary
The Kinetic Data of Bio-molecular Interaction database (KDBI) provides crucial experimental kinetic data for biomolecular interactions. Recent updates significantly expand its data and accessibility for biological system studies.
Area of Science:
- Biochemistry
- Systems Biology
- Bioinformatics
Background:
- Understanding biomolecular interaction kinetics is vital for studying cellular processes and simulating biological systems.
- Existing databases may lack comprehensive, experimentally determined kinetic data.
- Quantitative analysis of biological systems necessitates accurate kinetic parameters.
Purpose of the Study:
- To update and enhance the Kinetic Data of Bio-molecular Interaction database (KDBI).
- To improve data accessibility and searchability for researchers.
- To provide a comprehensive resource for biomolecular interaction kinetics.
Main Methods:
- Curating and integrating experimentally determined kinetic data from scientific literature.
- Implementing new data access methods, including pathway and molecule names.
- Providing data in System Biology Markup Language (SBML) format.
- Enhancing the search engine for more efficient data retrieval.
- Incorporating published parameter sets for simulation models.
Main Results:
- KDBI now contains 19,263 entries, a 2.3-fold increase.
- The database includes 10,532 distinct biomolecular binding and 11,954 interaction events.
- Data covers interactions involving 2635 proteins, 847 nucleic acids, 1603 small molecules, and 45 multi-step processes.
- Improved search functionality and SBML data format enhance usability.
Conclusions:
- The updated KDBI is a significantly expanded and more accessible resource for biomolecular interaction kinetics.
- It supports quantitative studies and simulations of biological systems.
- KDBI facilitates research in cellular processes and molecular events through readily available kinetic data.
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