List of liquid–liquid phase separation databases explained

Liquid-liquid phase separation (LLPS) is well defined in the Biomolecular condensate page.

LLPS databases cover different aspects of LLPS phenomena, ranging from cellular location of the Membraneless Organelles (MLOs) to the role of a particular protein/region forming the condensate state. These databases contain manually curated data supported by experimental evidence in the literature and can include related features as presence of protein disorder, low complexity, post-translational modifications, experimental details, phase diagrams, among others.

Table 1!Database!Created!Records!Description - Type of data
PhaSepDB2.0[1] 20192957Aims at collecting proteins that were found in membraneless organelles (MLOs), and organizes its entries according to MLO location. All entries can be classified into three groups depending on the quality of annotation: (i) Reviewed, verified by PhaSepDB curators, (ii) UniProtKB reviewed, pulled from UniProtKB, and (iii) high-throughput, identified by high-throughput experiments - MLO localization/association
MloDisDB[2] 2021771Manually curated database, developed by the same research group of PhaSepDB, but focusing on the association between MLOs and diseases - MLO localization/association and diseases
PhaSePro[3] 2019121Manually curated database of LLPS drivers, solely based on experimentally verified cases of LLPS - Drivers/Scaffolds
LLPSDB[4] 20191182Collection of in vitro LLPS experiments detailing the outcome and parameters of thousands of experiments -Experiments
DrLLPS[5] 20199285Database of LLPS proteins from nine model organisms - Clients, regulators, drivers/scaffolds

See also

References

  1. You. Kaiqiang. Huang. Qi. Yu. Chunyu. Shen. Boyan. Sevilla. Cristoffer. Shi. Minglei. Hermjakob. Henning. Chen. Yang. Li. Tingting. 2019-10-04. PhaSepDB: a database of liquid–liquid phase separation related proteins. Nucleic Acids Research. 48. D1. D354–D359. 10.1093/nar/gkz847. 0305-1048. 6943039. 31584089.
  2. Hou. Chao. Xie. Haotai. Fu. Yang. Ma. Yao. Li. Tingting. 2020-10-30. MloDisDB: a manually curated database of the relations between membraneless organelles and diseases. Briefings in Bioinformatics. 22. 4. 10.1093/bib/bbaa271. 33126250. 1467-5463.
  3. Mészáros. Bálint. Erdős. Gábor. Szabó. Beáta. Schád. Éva. Tantos. Ágnes. Abukhairan. Rawan. Horváth. Tamás. Murvai. Nikoletta. Kovács. Orsolya P. Kovács. Márton. Tosatto. Silvio C E. 2019-10-15. PhaSePro: the database of proteins driving liquid–liquid phase separation. Nucleic Acids Research. 48. D1. D360–D367. 10.1093/nar/gkz848. 0305-1048. 7145634. 31612960.
  4. Li. Qian. Peng. Xiaojun. Li. Yuanqing. Tang. Wenqin. Zhu. Jia’an. Huang. Jing. Qi. Yifei. Zhang. Zhuqing. 2019-09-06. LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro. Nucleic Acids Research. 48. D1. D320–D327. 10.1093/nar/gkz778. 0305-1048. 6943074. 31906602.
  5. Ning. Wanshan. Guo. Yaping. Lin. Shaofeng. Mei. Bin. Wu. Yu. Jiang. Peiran. Tan. Xiaodan. Zhang. Weizhi. Chen. Guowei. Peng. Di. Chu. Liang. 2020-01-08. DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes. Nucleic Acids Research. 48. D1. D288–D295. 10.1093/nar/gkz1027. 0305-1048. 7145660. 31691822.

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