Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, B1876BXD, Buenos Aires, Argentina.
Bioinformatics. 2013 Oct 1;29(19):2512-4. doi: 10.1093/bioinformatics/btt405. Epub 2013 Jul 11.
Conformational diversity is a key concept in the understanding of different issues related with protein function such as the study of catalytic processes in enzymes, protein-protein recognition, protein evolution and the origins of new biological functions. Here, we present a database of proteins with different degrees of conformational diversity. Conformational Diversity of Native State (CoDNaS) is a redundant collection of three-dimensional structures for the same protein derived from protein data bank. Structures for the same protein obtained under different crystallographic conditions have been associated with snapshots of protein dynamism and consequently could characterize protein conformers. CoDNaS allows the user to explore global and local structural differences among conformers as a function of different parameters such as presence of ligand, post-translational modifications, changes in oligomeric states and differences in pH and temperature. Additionally, CoDNaS contains information about protein taxonomy and function, disorder level and structural classification offering useful information to explore the underlying mechanism of conformational diversity and its close relationship with protein function. Currently, CoDNaS has 122 122 structures integrating 12 684 entries, with an average of 9.63 conformers per protein.
The database is freely available at http://www.codnas.com.ar/.
构象多样性是理解与蛋白质功能相关的不同问题的关键概念,例如研究酶的催化过程、蛋白质-蛋白质识别、蛋白质进化和新生物功能的起源。在这里,我们展示了一个具有不同构象多样性程度的蛋白质数据库。天然状态构象多样性(CoDNaS)是从蛋白质数据库中为同一蛋白质衍生的三维结构的冗余集合。在不同晶体学条件下获得的同一蛋白质的结构与蛋白质动力学的快照相关联,因此可以表征蛋白质构象。CoDNaS 允许用户探索构象之间的全局和局部结构差异,作为不同参数的函数,例如配体的存在、翻译后修饰、寡聚状态的变化以及 pH 值和温度的差异。此外,CoDNaS 包含有关蛋白质分类学和功能、无序水平和结构分类的信息,提供了有用的信息来探索构象多样性的潜在机制及其与蛋白质功能的密切关系。目前,CoDNaS 有 122 122 个结构,包含 12 684 个条目,每个蛋白质的平均构象数为 9.63 个。
该数据库可免费在 http://www.codnas.com.ar/ 获取。