Department of Biomedical Sciences, University of Padua Viale G. Colombo 3, Padova 35121, Italy.
CNR Institute of Neuroscience Viale G. Colombo 3, Padova 35121, Italy.
Bioinformatics. 2018 Jan 1;34(1):122-123. doi: 10.1093/bioinformatics/btx592.
The structures contained in the Protein Data Bank (PDB) database are of paramount importance to define our knowledge of folded proteins. While providing mainly circumstantial evidence, PDB data is also increasingly used to define the lack of unique structure, represented by mobile regions and even intrinsic disorder (ID). However, alternative definitions are used by different authors and potentially limit the generality of the analyses being carried out.
Here we present Mobi 2.0, a completely re-written version of the Mobi software for the determination of mobile and potentially disordered regions from PDB structures. Mobi 2.0 provides robust definitions of mobility based on four main sources of information: (i) missing residues, (ii) residues with high temperature factors, (iii) mobility between different models of the same structure and (iv) binding to another protein or nucleotide chain. Mobi 2.0 is well suited to aggregate information across different PDB structures for the same UniProt protein sequence, providing consensus annotations. The software is expected to standardize the treatment of mobility, allowing an easier comparison across different studies related to ID.
Mobi 2.0 provides the structure-based annotation for the MobiDB database. The software is available from URL http://protein.bio.unipd.it/mobi2/.
蛋白质数据库（PDB）中包含的结构对于定义我们对折叠蛋白质的认识至关重要。虽然主要提供间接证据，但 PDB 数据也越来越多地用于定义缺乏独特结构的区域，这些区域包括移动区域甚至固有无序（ID）。然而，不同的作者使用不同的定义，这可能限制了正在进行的分析的普遍性。
这里我们展示了 Mobi 2.0，这是用于从 PDB 结构中确定移动和潜在无序区域的 Mobi 软件的完全重写版本。Mobi 2.0 基于四个主要信息来源提供了强大的移动性定义：（i）缺失的残基，（ii）高温度因子的残基，（iii）同一结构不同模型之间的移动性，以及（iv）与另一个蛋白质或核苷酸链的结合。Mobi 2.0 非常适合聚合同一 UniProt 蛋白质序列的不同 PDB 结构中的信息，提供共识注释。该软件有望标准化对移动性的处理，允许更容易地比较与 ID 相关的不同研究。
Mobi 2.0 为 MobiDB 数据库提供基于结构的注释。该软件可从 URL http://protein.bio.unipd.it/mobi2/ 获得。
