KDBI: Kinetic data of Bio-molecular interactions database

Z. L. Ji, X. Chen, C. J. Zhen, Lixia Yao, L. Y. Han, W. K. Yeo, P. C. Chung, H. S. Puy, Y. T. Tay, A. Muhammad, Y. Z. Chen

Research output: Contribution to journalReview article

30 Citations (Scopus)

Abstract

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references. The kinetic data is in terms of one or a combination of the following quantities as given in the literature of a particular event: association/dissociation or on/off rate constant, first/second/third/... order rate constant, equilibrium rate constant, catalytic rate constant, equilibrium association/dissociation constant, inhibition constant and binding affinity constant. Each entry can be retrieved through protein or nucleic acid or ligand name, SWISS-PROT AC number, ligand CAS number and full-text search of a binding or reaction event. KDBI currently contains 8273 entries of biomolecular binding or reaction events involving 1380 proteins, 143 nucleic acids and 1395 small molecules. Hyperlinks are provided for accessing references in Medline and available 3D structures in PDB and NDB. This database can be accessed at http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp.

Original languageEnglish (US)
Pages (from-to)255-257
Number of pages3
JournalNucleic Acids Research
Volume31
Issue number1
DOIs
StatePublished - Jan 1 2003
Externally publishedYes

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Chemical Databases
Ligands
Databases
Proteins
Protein Databases
Nucleic Acids
Names
RNA
DNA
Viperidae

ASJC Scopus subject areas

  • Genetics

Cite this

Ji, Z. L., Chen, X., Zhen, C. J., Yao, L., Han, L. Y., Yeo, W. K., ... Chen, Y. Z. (2003). KDBI: Kinetic data of Bio-molecular interactions database. Nucleic Acids Research, 31(1), 255-257. https://doi.org/10.1093/nar/gkg067

KDBI : Kinetic data of Bio-molecular interactions database. / Ji, Z. L.; Chen, X.; Zhen, C. J.; Yao, Lixia; Han, L. Y.; Yeo, W. K.; Chung, P. C.; Puy, H. S.; Tay, Y. T.; Muhammad, A.; Chen, Y. Z.

In: Nucleic Acids Research, Vol. 31, No. 1, 01.01.2003, p. 255-257.

Research output: Contribution to journalReview article

Ji, ZL, Chen, X, Zhen, CJ, Yao, L, Han, LY, Yeo, WK, Chung, PC, Puy, HS, Tay, YT, Muhammad, A & Chen, YZ 2003, 'KDBI: Kinetic data of Bio-molecular interactions database', Nucleic Acids Research, vol. 31, no. 1, pp. 255-257. https://doi.org/10.1093/nar/gkg067
Ji, Z. L. ; Chen, X. ; Zhen, C. J. ; Yao, Lixia ; Han, L. Y. ; Yeo, W. K. ; Chung, P. C. ; Puy, H. S. ; Tay, Y. T. ; Muhammad, A. ; Chen, Y. Z. / KDBI : Kinetic data of Bio-molecular interactions database. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 1. pp. 255-257.
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