ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

被引:76
作者
Agostini, Federico [1 ,2 ]
Cirillo, Davide [1 ,2 ]
Maria Livi, Carmen [1 ,2 ]
Delli Ponti, Riccardo [1 ,2 ]
Gaetano Tartaglia, Gian [1 ,2 ]
机构
[1] Ctr Genom Regulat CRG, Barcelona 08003, Spain
[2] UPF, Barcelona 08003, Spain
基金
欧洲研究理事会;
关键词
PROTEIN SOLUBILITY; AGGREGATION; SEQUENCES;
D O I
10.1093/bioinformatics/btu420
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
A Summary: Here we introduce ccSOL omics, a webserver for largescale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis. Results: Using coil/disorder, hydrophobicity, hydrophilicity, beta-sheet and alpha-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31760 proteins sharing <30% sequence similarity.
引用
收藏
页码:2975 / 2977
页数:3
相关论文
共 23 条
  • [1] Sequence-Based Prediction of Protein Solubility
    Agostini, Federico
    Vendruscolo, Michele
    Tartaglia, Gian Gaetano
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2012, 421 (2-3) : 237 - 241
  • [2] Dynamic Transcriptional Response of Escherichia coli to Inclusion Body Formation
    Baig, Faraz
    Fernando, Lawrence P.
    Salazar, Mary Alice
    Powell, Rhonda R.
    Bruce, Terri F.
    Harcum, Sarah W.
    [J]. BIOTECHNOLOGY AND BIOENGINEERING, 2014, 111 (05) : 980 - 999
  • [3] Recombinant protein folding and misfolding in Escherichia coli
    Baneyx, F
    Mujacic, M
    [J]. NATURE BIOTECHNOLOGY, 2004, 22 (11) : 1399 - 1408
  • [4] Predicting protein associations with long noncoding RNAs
    Bellucci, Matteo
    Agostini, Federico
    Masin, Marianela
    Tartaglia, Gian Gaetano
    [J]. NATURE METHODS, 2011, 8 (06) : 444 - 445
  • [5] The protein structure initiative structural genomics knowledgebase
    Berman, Helen M.
    Westbrook, John D.
    Gabanyi, Margaret J.
    Tao, Wendy
    Shah, Raship
    Kouranov, Andrei
    Schwede, Torsten
    Arnold, Konstantin
    Kiefer, Florian
    Bordoli, Lorenza
    Kopp, Jrgen
    Podvinec, Michael
    Adams, Paul D.
    Carter, Lester G.
    Minor, Wladek
    Nair, Rajesh
    Baer, Joshua La
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D365 - D368
  • [6] RNA-mediated chaperone type for de novo protein folding
    Choi, Seong Il
    Ryu, Kisun
    Seong, Baik L.
    [J]. RNA BIOLOGY, 2009, 6 (01) : 21 - 24
  • [7] Discovery of protein-RNA networks
    Cirillo, Davide
    Maria Livi, Carmen
    Agostini, Federico
    Gaetano Tartaglia, Gian
    [J]. MOLECULAR BIOSYSTEMS, 2014, 10 (07) : 1632 - 1642
  • [8] AGGRESCAN:: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
    Conchillo-Sole, Oscar
    de Groot, Natalia S.
    Aviles, Francesc X.
    Vendrell, Josep
    Daura, Xavier
    Ventura, Salvador
    [J]. BMC BIOINFORMATICS, 2007, 8 (1)
  • [9] Role of Prion Protein Aggregation in Neurotoxicity
    Corsaro, Alessandro
    Thellung, Stefano
    Villa, Valentina
    Nizzari, Mario
    Florio, Tullio
    [J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2012, 13 (07): : 8648 - 8669
  • [10] Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    Fernandez-Escamilla, AM
    Rousseau, F
    Schymkowitz, J
    Serrano, L
    [J]. NATURE BIOTECHNOLOGY, 2004, 22 (10) : 1302 - 1306