LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro.
LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro.
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LLPSDB v2.0：体外进行液-液相分离的蛋白质的更新数据库
DOI：
10.1093/bioinformatics/btac026
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发表时间：
2022-03-28
期刊：
影响因子：
--
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Wang X;Zhou X;Yan Q;Liao S;Tang W;Xu P;Gao Y;Li Q;Dou Z;Yang W;Huang B;Li J;Zhang Z
越来越多的证据表明，蛋白质的液-液相分离（LLPS）在广泛的生物过程和相关疾病中起着至关重要的作用。蛋白质是否发生相分离不仅由生物分子本身的化学和物理性质决定，还受温度、离子强度、pH等环境条件以及被其他大分子排斥的体积等因素的调节。我们课题组最近开发了一个可web访问的数据库LLPSDB，该数据库从已发表的文献中综合整理了体外LLPS中涉及的所有蛋白及其相应的实验条件。随着生物分子LLPS研究的迅速增加和LLPSDB的日益普及，我们对数据库进行了更新，开发了新的LLPSDB v2.0版本。与之前发布的版本相比，数据内容增加了一倍以上，并增加了一个新的类别“Ambiguous system”。此外，改进了web界面，例如用户可以单独选择“相分离状态”选项或与其他选项组合进行数据库搜索。我们期望这个更新后的数据库将为用户提供更全面和有用的资源。LLPSDB v2.0可在http://bio-comp.org.cn/llpsdbv2免费获得。补充数据可在生物信息学网站获得。
Emerging evidences have suggested that liquid–liquid phase separation (LLPS) of proteins plays a vital role both in a wide range of biological processes and in related diseases. Whether a protein undergoes phase separation not only is determined by the chemical and physical properties of biomolecule themselves, but also is regulated by environmental conditions such as temperature, ionic strength, pH, as well as volume excluded by other macromolecules. A web accessible database LLPSDB was developed recently by our group, in which all the proteins involved in LLPS in vitro as well as corresponding experimental conditions were curated comprehensively from published literatures. With the rapid increase of investigations in biomolecular LLPS and growing popularity of LLPSDB, we updated the database, and developed a new version LLPSDB v2.0. In comparison of the previously released version, more than double contents of data are curated, and a new class ‘Ambiguous system’ is added. In addition, the web interface is improved, such as that users can search the database by selecting option ‘phase separation status’ alone or combined with other options. We anticipate that this updated database will serve as a more comprehensive and helpful resource for users. LLPSDB v2.0 is freely available at: http://bio-comp.org.cn/llpsdbv2. Supplementary data are available at Bioinformatics online.
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