LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro

Abstract

Summary 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. Availability and implementation LLPSDB v2.0 is freely available at: http://bio-comp.org.cn/llpsdbv2 Supplementary information Supplementary data are available at Bioinformatics online.

Protein conformation and biomolecular condensates

“…LLPSDB v2.0 (( Wang et al., 2022 ); http://bio-comp.org.cn/llpsdbv2 ) has incorporated 586 independent proteins and 6678 specific conditions, including intrinsically disordered and folded domains as well as complexes between proteins and between proteins and nucleic acids. Given that this database only incorporates proteins associated with in vitro experimental data, the magnitude of its content reflects the extraordinary interest that protein condensation has aroused.…”

Development and Validation of a Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Low-Grade Gliomas

“…The processed gene expression profiles based on RNA-sequencing technology were normalized used log2 (expression value + 0.01). The LLPS-related genes were obtained from LLPSDB v2.0 [ 19 ], and the only the unambiguous genes were included in our present study. As all data of the present are publicly available, ethical approval from the ethics committee of National Hospital of Guangxi Zhuang Autonomous Region was not necessary for the present study.…”

PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information

“…Several databases have been developed to contain information related to PS proteins, such as PS protein databases LLPSDB ( 19 ), PhaSePro ( 20 ) and DrLLPS ( 21 ), MLO-related protein databases RNAgranuleDB ( 22 ) and MSGP ( 23 ), and PS- and MLO-related disease database MloDisDB ( 24 ). Previously, we built the PS-related protein database PhaSepDB ( 25 ).…”