KDBI: Kinetic Data of Bio-molecular Interactions database
KDBI: Kinetic Data of Bio-molecular Interactions database
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DOI：
10.1093/nar/gkg067
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发表时间：
2003-01-01
影响因子：
14.9
通讯作者：
Chen, YZ
中科院分区：
文献类型：
--
作者：
Ji, ZL;Chen, X;Chen, YZ
了解细胞过程和潜在的分子事件需要了解分子相互作用的不同方面，分子网络和途径，以及所涉及的单个分子的序列，结构和功能。已经建立了相互作用分子、途径和相关化学反应方程的数据库。这些相互作用的动力学数据，这是重要的机制调查，定量研究和模拟的细胞过程和事件，是不提供在现有的数据库。我们介绍了一个新的生物分子相互作用动力学数据库（KDBI），旨在提供实验确定的蛋白质，蛋白质-RNA，蛋白质-DNA，蛋白质-配体，RNA-配体，DNA-配体结合或反应事件的动力学数据在文献中描述。KDBI包含有关结合或反应事件、参与分子（名称、同义词、分子式、分类、SWISS-PROT AC或CAS编号）、结合或反应方程、动力学数据和相关参考文献的信息。动力学数据是根据特定事件的文献中给出的以下量中的一个或组合：缔合/解离或开/关速率常数，第一/第二/第三/.有序速率常数、平衡速率常数、催化速率常数、平衡结合/解离常数、抑制常数和结合亲和力常数。每个条目可以通过蛋白质或核酸或配体名称、SWISS-PROT AC编号、配体CAS编号和结合或反应事件的全文检索来检索。KDBI目前包含8273个生物分子结合或反应事件条目，涉及1380种蛋白质、143种核酸和1395种小分子。提供超链接或访问Medline中的参考文献以及PDB和NDB中的可用3D结构。该数据库可在http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp上查阅。
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 or 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.