Table 4 Databases/datasets used to predict protein solubility (in chronological order)
# | Name | Reference | Size | Description | URL | ||
|---|---|---|---|---|---|---|---|
Total | Soluble | Insoluble | |||||
1 | Sd957 | [8] | 957 | 285 | 672 | It is made from 3 previous datasets: Idicula-Thomas et al. [28], Diaz et al. [20] and Chan et al. [1]. | |
2 | PROSO II | [6] | 82,000 | 41,000 | 41,000 | It is made from pepcDB and PDB and has been the largest dataset ever. It is balanced. | http://mips.helmholtz-muenchen.de/prosoII/img/Suppl_files.zip |
3 | HGPD | [33] | 17,821 (As of June 9th, 2011) | N/A | N/A | Human full-length cDNA. | |
4 | eSol | [25] | 30,173 | N/A | N/A | A database on the solubility of entire ensemble of E. coli proteins based on ASKA library. | |
5 | Solpro (SOLP) | [17] | 17,408 | 8704 | 8704 | It is collected from 4 different sources: PDB, SwissProt, TargetDB and dataset of “Idicula-Thomas, 2006”. The sequence redundancy is removed with 25% sequence similarity. It is balanced. | |
6 | PROSO | [19] | 14,000 | 7000 | 7000 | It is collected by merging 4 datasets: TargetDB, PDB and datasets of “Idicula-Thomas 2005” and “Idicula-Thomas 2006”. | - |
7 | pepcDB | [34] | N/A | N/A | N/A | It stored target and protocol information contributed by Protein Structure Initiative centres as well as targets imported from the TargetDB database. Now it has been replaced by TargetTrack. | |
8 | Idicula-Thomas 2006 | [27] | 192 | 62 | 139 | It is collected from the literature. | - |
9 | Idicula-Thomas 2005 | [28] | 174 | 41 | 133 | It is collected from the literature. | - |
10 | PDB | [35] | 91,359 (As of 11 June 2013) | N/A | N/A | It is a repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. | |
11 | SPINE | [16] | N/A | N/A | N/A | N/A | http://spine.nesg.org/user_login.cgi?url=http://spine.nesg.org/front_page.cgi? |
12 | TargetDB | [36] | 295,041 (As of 29 March 2013) | N/A | N/A | It provided status information on target sequences and tracks their progress through the various stages of protein production and structure determination. Now it has been replaced by TargetTrack. | |
13 | TargetTrack | - | 316,424 (As of 14 June 2013) | N/A | N/A | It is a target registration database which provides information on the experimental progress and status of targets selected for structural determination by the Protein Structure Initiative and other worldwide high-throughput structural biology projects. | |