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List of liquid–liquid phase separation databases

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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] 2019 2957 Aims 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] 2021 771 Manually 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] 2019 121 Manually curated database of LLPS drivers, solely based on experimentally verified cases of LLPS - Drivers/Scaffolds
LLPSDB[4] 2019 1182 Collection of in vitro LLPS experiments detailing the outcome and parameters of thousands of experiments -Experiments
DrLLPS[5] 2019 9285 Database of LLPS proteins from nine model organisms - Clients, regulators, drivers/scaffolds

See also

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References

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  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. doi:10.1093/nar/gkz847. ISSN 0305-1048. PMC 6943039. PMID 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). doi:10.1093/bib/bbaa271. ISSN 1467-5463. PMID 33126250.
  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. doi:10.1093/nar/gkz848. ISSN 0305-1048. PMC 7145634. PMID 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. doi:10.1093/nar/gkz778. ISSN 0305-1048. PMC 6943074. PMID 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. doi:10.1093/nar/gkz1027. ISSN 0305-1048. PMC 7145660. PMID 31691822.
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