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[KiBank: a database for computer-aided drug design based on protein-chemical interaction analysis]
Masahiro Aizawa1, Kenji Onodera, Junwei Zhang
1Collaborative Research Center of Frontier Simulation Software for Industrial Science, Institute of Industrial Science, University of Tokyo, Japan. aizawa@fsis.iis.u-tokyo.ac.jp
Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
|September 2, 2004
Summary
KiBank is a free database for computer-aided drug design, offering chemical and protein structures with binding affinities. It aids in silico binding studies by providing optimized structural data and inhibition constants (Ki) for over 5000 chemicals.
Area of Science:
- Computational chemistry
- Structural biology
- Pharmacology
Context:
- Databases are crucial for organizing and disseminating scientific data.
- Computer-aided drug design (CADD) relies on structural and affinity data.
- Inhibition constant (Ki) is a key metric for drug efficacy.
Purpose:
- To introduce KiBank, a comprehensive database for CADD.
- To provide researchers with optimized chemical and protein structures for in silico studies.
- To facilitate the comparison of chemical-protein binding strengths using Ki values.
Summary:
- KiBank is a freely accessible web database containing chemical structures, target protein structures, and binding affinity data, including inhibition constants (Ki).
- Structural data is optimized via energy minimization and stored in PDB or MDL MOL formats for direct use in in silico binding studies.
- As of April 2004, the database included 142 proteins, over 5000 chemicals, and over 6000 binding affinity values, primarily for membrane and nuclear receptors, with ongoing expansion.
Impact:
- Enables efficient in silico drug design and discovery.
- Supports research in pharmacology and structural biology by providing readily usable data.
- Facilitates the comparison and understanding of drug-target interactions.