Nucleic Acids Research, 2003, Vol. 31, No. 13 3701-3708
© 2003 Oxford University Press
GlobPlot: exploring protein sequences for globularity and disorder
European Molecular Biology Laboratory, Biocomputing Unit, D-69117 Heidelberg, Germany
*To whom correspondence should be addressed. Tel: +49 6221387451; Fax: +49 6221387517; Email: linding{at}embl.de
A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface—GlobPipe—for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. A. Encinar, G. Fernandez-Ballester, I. E. Sanchez, E. Hurtado-Gomez, F. Stricher, P. Beltrao, and L. Serrano ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs Bioinformatics, September 15, 2009; 25(18): 2418 - 2424. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Van Doorslaer, A. Ould M'hamed Ould Sidi, K. Zanier, V. Rybin, F. Deryckere, A. Rector, R. D. Burk, E. K. Lienau, M. van Ranst, and G. Trave Identification of Unusual E6 and E7 Proteins within Avian Papillomaviruses: Cellular Localization, Biophysical Characterization, and Phylogenetic Analysis J. Virol., September 1, 2009; 83(17): 8759 - 8770. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. S. H. Tan, B. Bodenmiller, A. Pasculescu, M. Jovanovic, M. O. Hengartner, C. Jorgensen, G. D. Bader, R. Aebersold, T. Pawson, and R. Linding Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases Sci. Signal., July 28, 2009; 2(81): ra39 - ra39. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. T. M. Mooij, E. Mitsiki, and A. Perrakis ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments Nucleic Acids Res., July 1, 2009; 37(suppl_2): W402 - W405. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Milbradt, S. Auerochs, H. Sticht, and M. Marschall Cytomegaloviral proteins that associate with the nuclear lamina: components of a postulated nuclear egress complex J. Gen. Virol., March 1, 2009; 90(3): 579 - 590. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Yin, F. Bangs, I. R. Paton, A. Prescott, J. James, M. G. Davey, P. Whitley, G. Genikhovich, U. Technau, D. W. Burt, et al. The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation Development, February 15, 2009; 136(4): 655 - 664. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Miller, L. J. Jensen, F. Diella, C. Jorgensen, M. Tinti, L. Li, M. Hsiung, S. A. Parker, J. Bordeaux, T. Sicheritz-Ponten, et al. Linear Motif Atlas for Phosphorylation-Dependent Signaling Sci. Signal., September 2, 2008; 1(35): ra2 - ra2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Rotem, C. Katz, H. Benyamini, M. Lebendiker, D. Veprintsev, S. Rudiger, T. Danieli, and A. Friedler The Structure and Interactions of the Proline-rich Domain of ASPP2 J. Biol. Chem., July 4, 2008; 283(27): 18990 - 18999. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. M. Overton, C. A. J. van Niekerk, L. G. Carter, A. Dawson, D. M. A. Martin, S. Cameron, S. A. McMahon, M. F. White, W. N. Hunter, J. H. Naismith, et al. TarO: a target optimisation system for structural biology Nucleic Acids Res., July 1, 2008; 36(suppl_2): W190 - W196. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. W. Brandt, J. Heringa, and J. A. M. Leunissen SEQATOMS: a web tool for identifying missing regions in PDB in sequence context Nucleic Acids Res., July 1, 2008; 36(suppl_2): W255 - W259. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. P. Fagan, M. A. Lambert, and S. G. J. Smith The Hek Outer Membrane Protein of Escherichia coli Strain RS218 Binds to Proteoglycan and Utilizes a Single Extracellular Loop for Adherence, Invasion, and Autoaggregation Infect. Immun., March 1, 2008; 76(3): 1135 - 1142. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. V. Tetko, I. V. Rodchenkov, M. C. Walter, T. Rattei, and H.-W. Mewes Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information Bioinformatics, March 1, 2008; 24(5): 621 - 628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Michael, G. Trave, C. Ramu, C. Chica, and T. J. Gibson Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation Bioinformatics, February 15, 2008; 24(4): 453 - 457. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Hou, R. Liu, S. Ross, E. J. Smart, H. Zhu, and W. Gong Crystallographic Studies of Human MitoNEET J. Biol. Chem., November 16, 2007; 282(46): 33242 - 33246. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Schlessinger, M. Punta, and B. Rost Natively unstructured regions in proteins identified from contact predictions Bioinformatics, September 15, 2007; 23(18): 2376 - 2384. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. P. John, T. Wang, S. Steffen, S. Longhi, C. S. Schmaljohn, and C. B. Jonsson Ebola Virus VP30 Is an RNA Binding Protein J. Virol., September 1, 2007; 81(17): 8967 - 8976. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hirose, K. Shimizu, S. Kanai, Y. Kuroda, and T. Noguchi POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions Bioinformatics, August 15, 2007; 23(16): 2046 - 2053. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Ishijima, N. Nagasaki, M. Maeshima, and M. Miyano RVCaB, a Calcium-binding Protein in Radish Vacuoles, is Predominantly an Unstructured Protein with a Polyproline Type II Helix J. Biochem., August 1, 2007; 142(2): 201 - 211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Watanabe, M. Shionyu, T. Kimura, K. Kimata, and H. Watanabe Splicing Factor 3b Subunit 4 Binds BMPR-IA and Inhibits Osteochondral Cell Differentiation J. Biol. Chem., July 13, 2007; 282(28): 20728 - 20738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-T. Su, C.-Y. Chen, and C.-M. Hsu iPDA: integrated protein disorder analyzer Nucleic Acids Res., July 13, 2007; 35(suppl_2): W465 - W472. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Cheng DOMAC: an accurate, hybrid protein domain prediction server Nucleic Acids Res., July 13, 2007; 35(suppl_2): W354 - W356. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fuxreiter, P. Tompa, and I. Simon Local structural disorder imparts plasticity on linear motifs Bioinformatics, April 15, 2007; 23(8): 950 - 956. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Thusberg and M. Vihinen The structural basis of hyper IgM deficiency - CD40L mutations Protein Eng. Des. Sel., March 1, 2007; 20(3): 133 - 141. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Min, K. H. Kirsch, Y. Zhao, S. Jeay, A. H. Palamakumbura, P. C. Trackman, and G. E. Sonenshein The Tumor Suppressor Activity of the Lysyl Oxidase Propeptide Reverses the Invasive Phenotype of Her-2/neu-Driven Breast Cancer Cancer Res., February 1, 2007; 67(3): 1105 - 1112. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Ragni, A. Coluccio, E. Rolli, J. M. Rodriguez-Pena, G. Colasante, J. Arroyo, A. M. Neiman, and L. Popolo GAS2 and GAS4, a Pair of Developmentally Regulated Genes Required for Spore Wall Assembly in Saccharomyces cerevisiae Eukaryot. Cell, February 1, 2007; 6(2): 302 - 316. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Neduva and R. B. Russell Proline-Rich Regions in Transcriptional Complexes: Heading in Many Directions Sci. Signal., January 16, 2007; 2007(369): pe1 - pe1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Kedzierska, L.-Y. Lian, and F. Hayes Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression Nucleic Acids Res., January 12, 2007; 35(1): 325 - 339. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Nooh, R. K. Aziz, M. Kotb, A. Eroshkin, W.-J. Chuang, T. Proft, and R. Kansal Streptococcal Mitogenic Exotoxin, SmeZ, Is the Most Susceptible M1T1 Streptococcal Superantigen to Degradation by the Streptococcal Cysteine Protease, SpeB J. Biol. Chem., November 17, 2006; 281(46): 35281 - 35288. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. D. Shaffer, G. Cenci, B. Thompson, G. E. Stephens, E. E. Slawson, K. Adu-Wusu, M. Gatti, and S. C. R. Elgin The Large Isoform of Drosophila melanogaster Heterochromatin Protein 2 Plays a Critical Role in Gene Silencing and Chromosome Structure Genetics, November 1, 2006; 174(3): 1189 - 1204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bottcher, B. G. Klupp, H. Granzow, W. Fuchs, K. Michael, and T. C. Mettenleiter Identification of a 709-Amino-Acid Internal Nonessential Region within the Essential Conserved Tegument Protein (p)UL36 of Pseudorabies Virus J. Virol., October 1, 2006; 80(19): 9910 - 9915. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Matsumura, K. Izui, and K. Mizuguchi A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment Protein Eng. Des. Sel., September 1, 2006; 19(9): 409 - 419. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Chen, W. Wang, S. Ling, C. Jia, and F. Wang KemaDom: a web server for domain prediction using kernel machine with local context. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W158 - W163. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Vullo, O. Bortolami, G. Pollastri, and S. C. E. Tosatto Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W164 - W168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Neduva and R. B. Russell DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W350 - W355. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. J. Li, M. Kawazaki, K. Ogasahara, and A. Nakagawa The Intracellular Region of ClC-3 Chloride Channel Is in a Partially Folded State and a Monomer. J. Biochem., May 1, 2006; 139(5): 813 - 820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Shojania and J. D. O'Neil HIV-1 Tat Is a Natively Unfolded Protein: THE SOLUTION CONFORMATION AND DYNAMICS OF REDUCED HIV-1 Tat-(1-72) BY NMR SPECTROSCOPY J. Biol. Chem., March 31, 2006; 281(13): 8347 - 8356. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F.-C. Chen, S.-S. Wang, C.-J. Chen, W.-H. Li, and T.-J. Chuang Alternatively and Constitutively Spliced Exons Are Subject to Different Evolutionary Forces Mol. Biol. Evol., March 1, 2006; 23(3): 675 - 682. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Gewehr and R. Zimmer SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles Bioinformatics, January 15, 2006; 22(2): 181 - 187. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. Llorente, B. Garcia-Barreno, M. Calero, E. Camafeita, J. A. Lopez, S. Longhi, F. Ferron, P. F. Varela, and J. A. Melero Structural analysis of the human respiratory syncytial virus phosphoprotein: characterization of an {alpha}-helical domain involved in oligomerization J. Gen. Virol., January 1, 2006; 87(1): 159 - 169. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Hopitzan, A. J. Baines, and E. Kordeli Molecular Evolution of Ankyrin: Gain of Function in Vertebrates by Acquisition of an Obscurin/Titin-Binding-Related Domain Mol. Biol. Evol., January 1, 2006; 23(1): 46 - 55. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Wright, S. C. Smith, V. Joardar, S. Scherer, J. Jervis, A. Warren, R. F. Helm, and M. Potts UV Irradiation and Desiccation Modulate the Three-dimensional Extracellular Matrix of Nostoc commune (Cyanobacteria) J. Biol. Chem., December 2, 2005; 280(48): 40271 - 40281. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Bao, W. Zhang, R. Krencik, H. Deng, Y. Wang, J. Girton, J. Johansen, and K. M. Johansen The JIL-1 kinase interacts with lamin Dm0 and regulates nuclear lamina morphology of Drosophila nurse cells J. Cell Sci., November 1, 2005; 118(21): 5079 - 5087. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. N. Khan and P. N. Lewis Unstructured Conformations Are a Substrate Requirement for the Sir2 Family of NAD-dependent Protein Deacetylases J. Biol. Chem., October 28, 2005; 280(43): 36073 - 36078. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. L. Gerloff, A. Creasey, S. Maslau, and R. Carter Structural models for the protein family characterized by gamete surface protein Pfs230 of Plasmodium falciparum PNAS, September 20, 2005; 102(38): 13598 - 13603. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. R. Yang, R. Thomson, P. McNeil, and R. M. Esnouf RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins Bioinformatics, August 15, 2005; 21(16): 3369 - 3376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Dosztanyi, V. Csizmok, P. Tompa, and I. Simon IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content Bioinformatics, August 15, 2005; 21(16): 3433 - 3434. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Prilusky, C. E. Felder, T. Zeev-Ben-Mordehai, E. H. Rydberg, O. Man, J. S. Beckmann, I. Silman, and J. L. Sussman FoldIndex(C): a simple tool to predict whether a given protein sequence is intrinsically unfolded Bioinformatics, August 15, 2005; 21(16): 3435 - 3438. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, and A. Godzik FFAS03: a server for profile-profile sequence alignments Nucleic Acids Res., July 1, 2005; 33(suppl_2): W284 - W288. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Li and I. S. Nathke Tumor-Associated NH2-Terminal Fragments Are the Most Stable Part of the Adenomatous Polyposis Coli Protein and Can Be Regulated by Interactions with COOH-Terminal Domains Cancer Res., June 15, 2005; 65(12): 5195 - 5204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. K. Saini and D. Fischer Meta-DP: domain prediction meta-server Bioinformatics, June 15, 2005; 21(12): 2917 - 2920. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Coeytaux and A. Poupon Prediction of unfolded segments in a protein sequence based on amino acid composition Bioinformatics, May 1, 2005; 21(9): 1891 - 1900. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ginalski, N. V. Grishin, A. Godzik, and L. Rychlewski Practical lessons from protein structure prediction Nucleic Acids Res., April 1, 2005; 33(6): 1874 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Ferron, C. Rancurel, S. Longhi, C. Cambillau, B. Henrissat, and B. Canard VaZyMolO: a tool to define and classify modularity in viral proteins J. Gen. Virol., March 1, 2005; 86(3): 743 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Vucetic, Z. Obradovic, V. Vacic, P. Radivojac, K. Peng, L. M. Iakoucheva, M. S. Cortese, J. D. Lawson, C. J. Brown, J. G. Sikes, et al. DisProt: a database of protein disorder Bioinformatics, January 1, 2005; 21(1): 137 - 140. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. G. Han, J. R. Smiley, C. Thomas, and L. J. Saif Genetic Recombination between Two Genotypes of Genogroup III Bovine Noroviruses (BoNVs) and Capsid Sequence Diversity among BoNVs and Nebraska-Like Bovine Enteric Caliciviruses J. Clin. Microbiol., November 1, 2004; 42(11): 5214 - 5224. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. Middleton, J. L. Parker, D. J. Richard, M. F. White, and C. S. Bond Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje Nucleic Acids Res., October 12, 2004; 32(18): 5442 - 5451. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. G. Diaz, T. Moldoveanu, M. J. Kuiper, R. L. Campbell, and P. L. Davies Insertion Sequence 1 of Muscle-specific Calpain, p94, Acts as an Internal Propeptide J. Biol. Chem., June 25, 2004; 279(26): 27656 - 27666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. A. Martin, G. Ausiello, B. Brannetti, A. Costantini, et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res., July 1, 2003; 31(13): 3625 - 3630. [Abstract] [Full Text] [PDF]
|
|