| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-106 91 Stockholm, Sweden
Reprint requests to: Arne Elofsson, Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-106 91 Stockholm, Sweden; e-mail: arne{at}sbc.su.se; fax: 468-5536 8512.
The ability to separate correct models of protein structures from less correct models is of the greatest importance for protein structure prediction methods. Several studies have examined the ability of different types of energy function to detect the native, or native-like, protein structure from a large set of decoys. In contrast to earlier studies, we examine here the ability to detect models that only show limited structural similarity to the native structure. These correct models are defined by the existence of a fragment that shows significant similarity between this model and the native structure. It has been shown that the existence of such fragments is useful for comparing the performance between different fold recognition methods and that this performance correlates well with performance in fold recognition. We have developed ProQ, a neural-network-based method to predict the quality of a protein model that extracts structural features, such as frequency of atom–atom contacts, and predicts the quality of a model, as measured either by LGscore or MaxSub. We show that ProQ performs at least as well as other measures when identifying the native structure and is better at the detection of correct models. This performance is maintained over several different test sets. ProQ can also be combined with the Pcons fold recognition predictor (Pmodeller) to increase its performance, with the main advantage being the elimination of a few high-scoring incorrect models. Pmodeller was successful in CASP5 and results from the latest LiveBench, LiveBench-6, indicating that Pmodeller has a higher specificity than Pcons alone.
Keywords: Homology modeling; fold recognition; structural information; LiveBench; neural networks; protein model; protein decoys
CiteULike 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Roovers, K. H. Kaminska, K. L. Tkaczuk, D. Gigot, L. Droogmans, and J. M. Bujnicki The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK) Nucleic Acids Res., June 1, 2008; 36(10): 3252 - 3262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Larsson, B. Wallner, E. Lindahl, and A. Elofsson Using multiple templates to improve quality of homology models in automated homology modeling Protein Sci., June 1, 2008; 17(6): 990 - 1002. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. White, Z. Li, R. Sardana, J. M. Bujnicki, E. M. Marcotte, and A. W. Johnson Bud23 Methylates G1575 of 18S rRNA and Is Required for Efficient Nuclear Export of Pre-40S Subunits Mol. Cell. Biol., May 15, 2008; 28(10): 3151 - 3161. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T.-A. Nguyen, M. Tychopoulos, F. Bichat, C. Zimmermann, J.-P. Flinois, M. Diry, E. Ahlberg, M. Delaforge, L. Corcos, P. Beaune, et al. Improvement of Cyclophosphamide Activation by CYP2B6 Mutants: From in Silico to ex Vivo Mol. Pharmacol., April 1, 2008; 73(4): 1122 - 1133. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. J. McGuffin The ModFOLD server for the quality assessment of protein structural models Bioinformatics, February 15, 2008; 24(4): 586 - 587. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Deladoey, N. Pfarr, J.-M. Vuissoz, J. Parma, G. Vassart, S. Biesterfeld, J. Pohlenz, and G. Van Vliet Pseudodominant Inheritance of Goitrous Congenital Hypothyroidism Caused by TPO Mutations: Molecular and in Silico Studies J. Clin. Endocrinol. Metab., February 1, 2008; 93(2): 627 - 633. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Haugstetter, M. A. Maurer, T. Blicher, M. Pagac, G. Wider, and L. Ellgaard Structure-Function Analysis of the Endoplasmic Reticulum Oxidoreductase TMX3 Reveals Interdomain Stabilization of the N-terminal Redox-active Domain J. Biol. Chem., November 16, 2007; 282(46): 33859 - 33867. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Almqvist, Y. Huang, A. Laaksonen, D.-N. Wang, and S. Hovmoller Docking and homology modeling explain inhibition of the human vesicular glutamate transporters Protein Sci., September 1, 2007; 16(9): 1819 - 1829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fasnacht, J. Zhu, and B. Honig Local quality assessment in homology models using statistical potentials and support vector machines Protein Sci., August 1, 2007; 16(8): 1557 - 1568. [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]
|
|
|
|
 |
|
 H. Klein, L. Garneau, U. Banderali, M. Simoes, L. Parent, and R. Sauve Structural Determinants of the Closed KCa3.1 Channel Pore in Relation to Channel Gating: Results from a Substituted Cysteine Accessibility Analysis J. Gen. Physiol., March 26, 2007; 129(4): 299 - 315. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Dlakic DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold Bioinformatics, November 15, 2006; 22(22): 2711 - 2714. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Lamani, R. B. Mewbourne, D. S. Fletcher, S. D. Maltsev, L. L. Danilov, V. V. Veselovsky, A. V. Lozanova, N. Ya. Grigorieva, O. A. Pinsker, J. Xing, et al. Structural studies and mechanism of Saccharomyces cerevisiae dolichyl-phosphate-mannose synthase: insights into the initial step of synthesis of dolichyl-phosphate-linked oligosaccharide chains in membranes of endoplasmic reticulum Glycobiology, July 1, 2006; 16(7): 666 - 678. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Eramian, M.-y. Shen, D. Devos, F. Melo, A. Sali, and M. A. Marti-Renom A composite score for predicting errors in protein structure models Protein Sci., July 1, 2006; 15(7): 1653 - 1666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Becker, V. Meyer, H. Madaoui, and R. Guerois Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response Bioinformatics, June 1, 2006; 22(11): 1289 - 1292. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Wallner and A. Elofsson Identification of correct regions in protein models using structural, alignment, and consensus information Protein Sci., April 1, 2006; 15(4): 900 - 913. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Wallner and A. Elofsson Pcons5: combining consensus, structural evaluation and fold recognition scores Bioinformatics, December 1, 2005; 21(23): 4248 - 4254. [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]
|
|
|
|
|
|
B. Wallner and A. Elofsson All are not equal: A benchmark of different homology modeling programs Protein Sci., May 1, 2005; 14(5): 1315 - 1327. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
