Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (139)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Lambert, C.
Right arrow Articles by Depiereux, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lambert, C.
Right arrow Articles by Depiereux, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 9 2002
Pages 1250-1256
© 2002 Oxford University Press

ESyPred3D: Prediction of proteins 3D structures

Christophe Lambert 1,*, Nadia Léonard 1, Xavier De Bolle 1 and Eric Depiereux 1

1 Facultés Universitaires Notre-Dame de la Paix, Unité de Recherche en Biologie Moléculaire, Rue de Bruxelles, 61, B-5000 Namur, Belgium

Received on February 1, 2002 ; revised on March 7, 2002 ; accepted on March 18, 2002

Motivation: Homology or comparative modeling is currently the most accurate method to predict the three-dimensional structure of proteins. It generally consists in four steps: (1) databanks searching to identify the structural homolog, (2) target–template alignment, (3) model building and optimization, and (4) model evaluation. The target–template alignment step is generally accepted as the most critical step in homology modeling.

Results: We present here ESyPred3D, a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three-dimensional structure is build using the modeling package MODELLER. ESyPred3D was tested on 13 targets in the CASP4 experiment (Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results compared to PSI-BLAST alignments and ESyPred3D alignments are among the most accurate compared to those of participants having used the same template.

Availability: ESyPred3D is available through its web site at http://www.fundp.ac.be/urbm/bioinfo/esypred/

Contact: christophe.lambert{at}fundp.ac.be http://www.fundp.ac.be/~lambertc

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
E. P. Tchesnokov, A. Obikhod, R. F. Schinazi, and M. Gotte
Engineering of a Chimeric RB69 DNA Polymerase Sensitive to Drugs Targeting the Cytomegalovirus Enzyme
J. Biol. Chem., September 25, 2009; 284(39): 26439 - 26446.
[Abstract] [Full Text] [PDF]

Home page
 Eur J EndocrinolHome page
S. Dateki, K. Hizukuri, T. Tanaka, N. Katsumata, P. Katavetin, and T. Ogata
An immunologically anomalous but considerably bioactive GH produced by a novel GH1 mutation (p.D116E)
Eur. J. Endocrinol., August 1, 2009; 161(2): 301 - 306.
[Abstract] [Full Text] [PDF]

Home page
 Acta Biochim Biophys SinHome page
H. Shi, L. Zhu, Y. Zhou, G. Li, L. Chen, and X. Li
A cotton gene encoding a polygalacturonase inhibitor-like protein is specifically expressed in petals
Acta Biochim Biophys Sin, April 1, 2009; 41(4): 316 - 324.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
D. Marcal, A. T. Rego, M. A. Carrondo, and F. J. Enguita
1,3-Propanediol Dehydrogenase from Klebsiella pneumoniae: Decameric Quaternary Structure and Possible Subunit Cooperativity
J. Bacteriol., February 15, 2009; 191(4): 1143 - 1151.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
C. Simpson, C. Thomas, K. Findlay, E. Bayer, and A. J. Maule
An Arabidopsis GPI-Anchor Plasmodesmal Neck Protein with Callose Binding Activity and Potential to Regulate Cell-to-Cell Trafficking
PLANT CELL, February 1, 2009; 21(2): 581 - 594.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. B. Luther, H. Schindelin, and R. S. Haltiwanger
Structural and Mechanistic Insights into Lunatic Fringe from a Kinetic Analysis of Enzyme Mutants
J. Biol. Chem., January 30, 2009; 284(5): 3294 - 3305.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
I. Mulako, J. M. Farrant, H. Collett, and N. Illing
Expression of Xhdsi-1VOC, a novel member of the vicinal oxygen chelate (VOC) metalloenzyme superfamily, is up-regulated in leaves and roots during desiccation in the resurrection plant Xerophyta humilis (Bak) Dur and Schinz
J. Exp. Bot., October 1, 2008; 59(14): 3885 - 3901.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
O. Samuelsen, M. Castanheira, T. R. Walsh, and J. Spencer
Kinetic Characterization of VIM-7, a Divergent Member of the VIM Metallo-{beta}-Lactamase Family
Antimicrob. Agents Chemother., August 1, 2008; 52(8): 2905 - 2908.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
N. Iritani, H. Vennema, J. J. Siebenga, R. J. Siezen, B. Renckens, Y. Seto, A. Kaida, and M. Koopmans
Genetic Analysis of the Capsid Gene of Genotype GII.2 Noroviruses
J. Virol., August 1, 2008; 82(15): 7336 - 7345.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
G. W. Moy, S. A. Springer, S. L. Adams, W. J. Swanson, and V. D. Vacquier
Extraordinary intraspecific diversity in oyster sperm bindin
PNAS, February 12, 2008; 105(6): 1993 - 1998.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. Arevalo, S. Shanmugasundararaj, M. F. Wilkemeyer, X. Dou, S. Chen, M. E. Charness, and K. W. Miller
An alcohol binding site on the neural cell adhesion molecule L1
PNAS, January 8, 2008; 105(1): 371 - 375.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Zhang, V. Brovkovych, S. Brovkovych, F. Tan, B.-S. Lee, T. Sharma, and R. A. Skidgel
Dynamic Receptor-dependent Activation of Inducible Nitric-oxide Synthase by ERK-mediated Phosphorylation of Ser745
J. Biol. Chem., November 2, 2007; 282(44): 32453 - 32461.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. Fernandez-Fuentes, B. K. Rai, C. J. Madrid-Aliste, J. Eduardo Fajardo, and A. Fiser
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
Bioinformatics, October 1, 2007; 23(19): 2558 - 2565.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, and K. R. Acharya
Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus xanthus and Its Complex with the Inhibitor Acifluorfen
J. Biol. Chem., December 15, 2006; 281(50): 38625 - 38633.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Jayaram, K. Bhushan, S. R. Shenoy, P. Narang, S. Bose, P. Agrawal, D. Sahu, and V. Pandey
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
Nucleic Acids Res., December 4, 2006; 34(21): 6195 - 6204.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. K. Rai, C. J. Madrid-Aliste, J. E. Fajardo, and A. Fiser
MMM: a sequence-to-structure alignment protocol
Bioinformatics, November 1, 2006; 22(21): 2691 - 2692.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-C. Chen, J.-K. Hwang, and J.-M. Yang
(PS)2: protein structure prediction server.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W152 - W157.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Arnold, L. Bordoli, J. Kopp, and T. Schwede
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
Bioinformatics, January 15, 2006; 22(2): 195 - 201.
[Abstract] [Full Text] [PDF]

Home page
 J. Am. Soc. Nephrol.Home page
X.-P. Wang, A. B. Fogo, S. Colon, G. Giannico, S. R. Abul-Ezz, J. H. Miner, and D.-B. Borza
Distinct Epitopes for Anti-Glomerular Basement Membrane Alport Alloantibodies and Goodpasture Autoantibodies within the Noncollagenous Domain of {alpha}3(IV) Collagen: A Janus-Faced Antigen
J. Am. Soc. Nephrol., December 1, 2005; 16(12): 3563 - 3571.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Pharmacol.Home page
P. Wellendorph, K. B. Hansen, A. Balsgaard, J. R. Greenwood, J. Egebjerg, and H. Brauner-Osborne
Deorphanization of GPRC6A: A Promiscuous L-{alpha}-Amino Acid Receptor with Preference for Basic Amino Acids
Mol. Pharmacol., March 1, 2005; 67(3): 589 - 597.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. M. Mayer and J. Shanklin
A Structural Model of the Plant Acyl-Acyl Carrier Protein Thioesterase FatB Comprises Two Helix/4-Stranded Sheet Domains, the N-terminal Domain Containing Residues That Affect Specificity and the C-terminal Domain Containing Catalytic Residues
J. Biol. Chem., February 4, 2005; 280(5): 3621 - 3627.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Endocrinol. Metab.Home page
M. Fukami, R. Horikawa, T. Nagai, T. Tanaka, Y. Naiki, N. Sato, T. Okuyama, H. Nakai, S. Soneda, K. Tachibana, et al.
Cytochrome P450 Oxidoreductase Gene Mutations and Antley-Bixler Syndrome with Abnormal Genitalia and/or Impaired Steroidogenesis: Molecular and Clinical Studies in 10 Patients
J. Clin. Endocrinol. Metab., January 1, 2005; 90(1): 414 - 426.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Kong, B. T. K. Lee, J. C. Tong, T. W. Tan, and S. Ranganathan
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W356 - W359.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Y. Y. Koh, V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M. S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, et al.
EVA: evaluation of protein structure prediction servers
Nucleic Acids Res., July 1, 2003; 31(13): 3311 - 3315.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Schwede, J. Kopp, N. Guex, and M. C. Peitsch
SWISS-MODEL: an automated protein homology-modeling server
Nucleic Acids Res., July 1, 2003; 31(13): 3381 - 3385.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.