Bioinformatics Vol. 19 no. 7 2003
Pages 874-881
© 2003 Oxford University Press
Improvement of the GenTHREADER method for genomic fold recognition
Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
Received on October 1, 2002
; revised on November 29, 2002
; accepted on December 14, 2002
Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins.
Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.
Availability: http://www.psipred.net
Contact: l.mcguffin{at}cs.ucl.ac.uk
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Chavez-Gutierrez, A. Tolia, E. Maes, T. Li, P. C. Wong, and B. de Strooper Glu332 in the Nicastrin Ectodomain Is Essential for {gamma}-Secretase Complex Maturation but Not for Its Activity J. Biol. Chem., July 18, 2008; 283(29): 20096 - 20105. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. I. Serysheva, S. J. Ludtke, M. L. Baker, Y. Cong, M. Topf, D. Eramian, A. Sali, S. L. Hamilton, and W. Chiu Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel PNAS, July 15, 2008; 105(28): 9610 - 9615. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. J. Sammut, R. D. Finn, and A. Bateman Pfam 10 years on: 10 000 families and still growing Brief Bioinform, May 1, 2008; 9(3): 210 - 219. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Yep, G. L. Kenyon, and M. J. McLeish Saturation mutagenesis of putative catalytic residues of benzoylformate decarboxylase provides a challenge to the accepted mechanism PNAS, April 15, 2008; 105(15): 5733 - 5738. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Anderson, D. Korkin, D. L. Smith, S. Makovets, J. J. Seidel, A. Sali, and E. H. Blackburn Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break Genes & Dev., April 1, 2008; 22(7): 854 - 859. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. A. Hoeberichts, E. Vaeck, G. Kiddle, E. Coppens, B. van de Cotte, A. Adamantidis, S. Ormenese, C. H. Foyer, M. Zabeau, D. Inze, et al. A Temperature-sensitive Mutation in the Arabidopsis thaliana Phosphomannomutase Gene Disrupts Protein Glycosylation and Triggers Cell Death J. Biol. Chem., February 29, 2008; 283(9): 5708 - 5718. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Melo and A. Sali Fold assessment for comparative protein structure modeling Protein Sci., November 1, 2007; 16(11): 2412 - 2426. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Ballicora, E. D. Erben, T. Yazaki, A. L. Bertolo, A. M. Demonte, J. R. Schmidt, M. Aleanzi, C. M. Bejar, C. M. Figueroa, C. M. Fusari, et al. Identification of Regions Critically Affecting Kinetics and Allosteric Regulation of the Escherichia coli ADP-Glucose Pyrophosphorylase by Modeling and Pentapeptide-Scanning Mutagenesis J. Bacteriol., July 15, 2007; 189(14): 5325 - 5333. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Wallner, P. Larsson, and A. Elofsson Pcons.net: protein structure prediction meta server Nucleic Acids Res., July 13, 2007; 35(suppl_2): W369 - W374. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Geslin, M. Gaillard, D. Flament, K. Rouault, M. Le Romancer, D. Prieur, and G. Erauso Analysis of the First Genome of a Hyperthermophilic Marine Virus-Like Particle, PAV1, Isolated from Pyrococcus abyssi J. Bacteriol., June 15, 2007; 189(12): 4510 - 4519. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. C. W. Avellar, L. Honda, K. G. Hamil, Y. Radhakrishnan, S. Yenugu, G. Grossman, P. Petrusz, F. S. French, and S. H. Hall Novel Aspects of the Sperm-Associated Antigen 11 (SPAG11) Gene Organization and Expression in Cattle (Bos taurus) Biol Reprod, June 1, 2007; 76(6): 1103 - 1116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Elkins, E. Papagrigoriou, G. Berridge, X. Yang, C. Phillips, C. Gileadi, P. Savitsky, and D. A. Doyle Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions Protein Sci., April 1, 2007; 16(4): 683 - 694. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Dalhus, I. H. Helle, P. H. Backe, I. Alseth, T. Rognes, M. Bjoras, and J. K. Laerdahl Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats Nucleic Acids Res., April 1, 2007; 35(7): 2451 - 2459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Xu, D. Song, L. C. Pedersen, and J. Liu Mutational Study of Heparan Sulfate 2-O-Sulfotransferase and Chondroitin Sulfate 2-O-Sulfotransferase J. Biol. Chem., March 16, 2007; 282(11): 8356 - 8367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Fariselli, I. Rossi, E. Capriotti, and R. Casadio The WWWH of remote homolog detection: The state of the art Brief Bioinform, March 1, 2007; 8(2): 78 - 87. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. D. Winn, R. Haimov-Kochman, A. C. Paquet, Y. J. Yang, M. S. Madhusudhan, M. Gormley, K.-T. V. Feng, D. A. Bernlohr, S. McDonagh, L. Pereira, et al. Gene Expression Profiling of the Human Maternal-Fetal Interface Reveals Dramatic Changes between Midgestation and Term Endocrinology, March 1, 2007; 148(3): 1059 - 1079. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. de la Vega, R. G. Sevilla, A. Hermoso, J. Lorenzo, S. Tanco, A. Diez, L. D. Fricker, J. M. Bautista, and F. X. Aviles Nna1-like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily FASEB J, March 1, 2007; 21(3): 851 - 865. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. O. Huising, E. J. W. Geven, C. P. Kruiswijk, S. B. Nabuurs, E. H. Stolte, F. A. T. Spanings, B. M. L. Verburg-van Kemenade, and G. Flik Increased Leptin Expression in Common Carp (Cyprinus carpio) after Food Intake But Not after Fasting or Feeding to Satiation Endocrinology, December 1, 2006; 147(12): 5786 - 5797. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Palecek, S. Vidot, M. Feng, A. J. Doherty, and A. R. Lehmann The Smc5-Smc6 DNA Repair Complex: BRIDGING OF THE Smc5-Smc6 HEADS BY THE KLEISIN, Nse4, AND NON-KLEISIN SUBUNITS J. Biol. Chem., December 1, 2006; 281(48): 36952 - 36959. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. B. Rubin, Y. Shemesh, M. Cohen, S. Elgavish, H. M. Robertson, and G. Bloch Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock Genome Res., November 1, 2006; 16(11): 1352 - 1365. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. L. de boer, D. A. Krupp, and V. M. Weis Two Atypical Carbonic Anhydrase Homologs From the Planula Larva of the Scleractinian Coral Fungia scutaria. Biol. Bull., August 1, 2006; 211(1): 18 - 30. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Pellegrini-Calace and A. Tramontano Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches Bioinformatics, April 1, 2006; 22(7): 775 - 778. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. G. Saerens, K. J. Verstrepen, S. D. M. Van Laere, A. R. D. Voet, P. Van Dijck, F. R. Delvaux, and J. M. Thevelein The Saccharomyces cerevisiae EHT1 and EEB1 Genes Encode Novel Enzymes with Medium-chain Fatty Acid Ethyl Ester Synthesis and Hydrolysis Capacity J. Biol. Chem., February 17, 2006; 281(7): 4446 - 4456. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B. T. Chait, M. P. Rout, and A. Sali Simple fold composition and modular architecture of the nuclear pore complex PNAS, February 14, 2006; 103(7): 2172 - 2177. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kurdyukov, A. Faust, C. Nawrath, S. Bar, D. Voisin, N. Efremova, R. Franke, L. Schreiber, H. Saedler, J.-P. Metraux, et al. The Epidermis-Specific Extracellular BODYGUARD Controls Cuticle Development and Morphogenesis in Arabidopsis PLANT CELL, February 1, 2006; 18(2): 321 - 339. [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]
|
|
|
|
|
|
R. Jordanova, G. Radoslavov, P. Fischer, A. Torda, F. Lottspeich, R. Boteva, R. D. Walter, I. Bankov, and E. Liebau The Highly Abundant Protein Ag-lbp55 from Ascaridia galli Represents a Novel Type of Lipid-binding Proteins J. Biol. Chem., December 16, 2005; 280(50): 41429 - 41438. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. B. Krieger and K. G. Ross Molecular Evolutionary Analyses of the Odorant-Binding Protein Gene Gp-9 in Fire Ants and Other Solenopsis Species Mol. Biol. Evol., October 1, 2005; 22(10): 2090 - 2103. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. J. McInnes, D. Deane, D. Haig, A. Percival, J. Thomson, and A. R. Wood Glycosylation, Disulfide Bond Formation, and the Presence of a WSXWS-Like Motif in the Orf Virus GIF Protein Are Critical for Maintaining the Integrity of Binding to Ovine Granulocyte-Macrophage Colony-Stimulating Factor and Interleukin-2 J. Virol., September 1, 2005; 79(17): 11205 - 11213. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Pettitt, L. J. McGuffin, and D. T. Jones Improving sequence-based fold recognition by using 3D model quality assessment Bioinformatics, September 1, 2005; 21(17): 3509 - 3515. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Bryson, L. J. McGuffin, R. L. Marsden, J. J. Ward, J. S. Sodhi, and D. T. Jones Protein structure prediction servers at University College London Nucleic Acids Res., July 1, 2005; 33(suppl_2): W36 - W38. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. K. Shah, P. Aloy, P. Bork, and R. B. Russell Structural similarity to bridge sequence space: Finding new families on the bridges Protein Sci., May 1, 2005; 14(5): 1305 - 1314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Ayalon, E. Segev, S. Elgavish, and Y. Stern-Bach Two Regions in the N-terminal Domain of Ionotropic Glutamate Receptor 3 Form the Subunit Oligomerization Interfaces That Control Subtype-specific Receptor Assembly J. Biol. Chem., April 15, 2005; 280(15): 15053 - 15060. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Zhang, S. Kochhar, and M. G. Grigorov Descriptor-based protein remote homology identification Protein Sci., February 1, 2005; 14(2): 431 - 444. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Rychlewski and D. Fischer LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction Protein Sci., January 1, 2005; 14(1): 240 - 245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Grohmanova, D. Schlaepfer, D. Hess, P. Gutierrez, M. Beck, and R. Kroschewski Phosphorylation of IQGAP1 Modulates Its Binding to Cdc42, Revealing a New Type of Rho-GTPase Regulator J. Biol. Chem., November 19, 2004; 279(47): 48495 - 48504. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Egelund, M. Skjot, N. Geshi, P. Ulvskov, and B. L. Petersen A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes Plant Physiology, September 1, 2004; 136(1): 2609 - 2620. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Uehara, T. Kawabata, and N. Go Filtering remote homologues using predicted structural information Protein Eng. Des. Sel., July 1, 2004; 17(7): 565 - 570. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Torda, J. B. Procter, and T. Huber Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices Nucleic Acids Res., July 1, 2004; 32(suppl_2): W532 - W535. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Paumann, B. Lubura, G. Regelsberger, M. Feichtinger, G. Kollensberger, C. Jakopitsch, P. G. Furtmuller, G. A. Peschek, and C. Obinger Soluble CuA Domain of Cyanobacterial Cytochrome c Oxidase J. Biol. Chem., March 12, 2004; 279(11): 10293 - 10303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Rodriguez, L. M. Quiros, and J. A. Salas MtmMII-mediated C-Methylation during Biosynthesis of the Antitumor Drug Mithramycin Is Essential for Biological Activity and DNA-Drug Interaction J. Biol. Chem., February 27, 2004; 279(9): 8149 - 8158. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. McGuffin, S. A. Street, K. Bryson, S.-A. Sorensen, and D. T. Jones The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms Nucleic Acids Res., January 1, 2004; 32(90001): D196 - 199. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. B. Kuznetsov and S. Rackovsky Similarity between the C-terminal domain of the prion protein and chimpanzee cytomegalovirus glycoprotein UL9 Protein Eng. Des. Sel., December 1, 2003; 16(12): 861 - 863. [Abstract] [Full Text] [PDF]
|
|