Protein Engineering vol. 7 no. 2 pp. 157-164, 1994
© 1994 Oxford University Press
RESEARCH-ARTICLE |
SOPM: a self-optimized method for protein secondary structure prediction
Institut de Biologie et de Chimie des Protéines, UPR 412-CNRS 7, Passage du Vercors, F-69367 Lyon cedex 07, France
1To whom correspondence should be adressed
A new method called the self-optimized prediction method (SOPM) has been developed to improve the success rate in the prediction of the secondary structure of proteins. This new method has been checked against an updated release of the Kabsch and Sander database, ‘DATABASE.DSSP’, comprising 239 protein chains. The first step of the SOPM is to build sub-databases of protein sequences and their known secondary structures drawn from ‘DATABASE.DSSP’ by (i) making binary comparisons of all protein sequences and (ii) taking into account the prediction of structural classes of proteins. The second step is to submit each protein of the sub-database to a secondary structure prediction using a predictive algorithm based on sequence similarity. The third step is to iteratively determine the predictive parameters that optimize the prediction quality on the whole sub-database. The last step is to apply the final parameters to the query sequence. This new method correctly predicts 69% of amino acids for a three-state description of the secondary structure (a helix, (3 sheet and coil) in the whole database (46 Oil amino acids). The correlation coefficients are Ca=0.54, Q=0.50 and Cc=0.48. Root mean square deviations of 10% in the secondary structure content are obtained. Implications for the users are drawn so as to derive an accuracy at the amino acid level and provide the user with a guide for secondary structure prediction. The SOPM method is available by anonymous ftp to ibcp.fr.
Keywords: amino acid sequence/hormology modelling/protein structure/secondary structure prediction
Received July 9, 1993; revised September 20, 1993; accepted October 15, 1993.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Z. Zhao, Y. Ma, C. Dai, R. Zhao, S. Li, Y. Wu, Z. Cao, and W. Li Imcroporin, a New Cationic Antimicrobial Peptide from the Venom of the Scorpion Isometrus maculates Antimicrob. Agents Chemother., August 1, 2009; 53(8): 3472 - 3477. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Qi, W. Shi, N. Xue, C. Pan, W. Jing, K. Liu, and S. Jiang Rationally Designed Anti-HIV Peptides Containing Multifunctional Domains as Molecule Probes for Studying the Mechanisms of Action of the First and Second Generation HIV Fusion Inhibitors J. Biol. Chem., October 31, 2008; 283(44): 30376 - 30384. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Torres and A. M. Espino Mapping of B-Cell Epitopes on a Novel 11.5-Kilodalton Fasciola hepatica-Schistosoma mansoni Cross-Reactive Antigen Belonging to a Member of the F. hepatica Saposin-Like Protein Family. Infect. Immun., August 1, 2006; 74(8): 4932 - 4938. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Weider, A. Machnik, F. Klebl, and N. Sauer Vhr1p, a New Transcription Factor from Budding Yeast, Regulates Biotin-dependent Expression of VHT1 and BIO5 J. Biol. Chem., May 12, 2006; 281(19): 13513 - 13524. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Moya, G. Perez de Nanclares, L. Castano, N. Potau, J. R. Bilbao, A. Carrascosa, M. Bargada, R. Coya, P. Martul, E. Vicens-Calvet, et al. Functional Study of a Novel Single Deletion in the TITF1/NKX2.1 Homeobox Gene That Produces Congenital Hypothyroidism and Benign Chorea But Not Pulmonary Distress J. Clin. Endocrinol. Metab., May 1, 2006; 91(5): 1832 - 1841. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Chatterjee, P. Sharma, and J. P. Khurana Cryptochrome 1 from Brassica napus Is Up-Regulated by Blue Light and Controls Hypocotyl/Stem Growth and Anthocyanin Accumulation Plant Physiology, May 1, 2006; 141(1): 61 - 74. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. N. Eidhin, A. W. Ryan, R. M. Doyle, J. B. Walsh, and D. Kelleher Sequence and phylogenetic analysis of the gene for surface layer protein, slpA, from 14 PCR ribotypes of Clostridium difficile J. Med. Microbiol., January 1, 2006; 55(1): 69 - 83. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Guyard, E. M. Chester, S. J. Raffel, M. E. Schrumpf, P. F. Policastro, S. F. Porcella, J. M. Leong, and T. G. Schwan Relapsing Fever Spirochetes Contain Chromosomal Genes with Unique Direct Tandemly Repeated Sequences Infect. Immun., May 1, 2005; 73(5): 3025 - 3037. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Borgatti, C. Zucca, A. Cavallini, M. Ferrario, C. Panzeri, P. Castaldo, M. V. Soldovieri, C. Baschirotto, N. Bresolin, B. D. Bernardina, et al. A novel mutation in KCNQ2 associated with BFNC, drug resistant epilepsy, and mental retardation Neurology, July 13, 2004; 63(1): 57 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Sillanpaa, Y. Xu, S. R. Nallapareddy, B. E. Murray, and M. Hook A family of putative MSCRAMMs from Enterococcus faecalis Microbiology, July 1, 2004; 150(7): 2069 - 2078. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Marco, A. Cuesta, L. Pedrola, F. Palau, and I. Marin Evolutionary and Structural Analyses of GDAP1, Involved in Charcot-Marie-Tooth Disease, Characterize a Novel Class of Glutathione Transferase-Related Genes Mol. Biol. Evol., January 1, 2004; 21(1): 176 - 187. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. Yudt, C. M. Jewell, R. J. Bienstock, and J. A. Cidlowski Molecular Origins for the Dominant Negative Function of Human Glucocorticoid Receptor Beta Mol. Cell. Biol., June 15, 2003; 23(12): 4319 - 4330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Paris, C. Viemon, G. Curien, and R. Dumas Mechanism of Control of Arabidopsis thaliana Aspartate Kinase-Homoserine Dehydrogenase by Threonine J. Biol. Chem., February 7, 2003; 278(7): 5361 - 5366. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Shiba, T. Shirai, T. Honma, and T. Noda Translated products of tandem microgene repeats exhibit diverse properties also seen in natural proteins Protein Eng. Des. Sel., January 1, 2003; 16(1): 57 - 63. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Chattopadhyay and S. Roy DnaK-Sigma 32 Interaction Is Temperature-dependent. IMPLICATION FOR THE MECHANISM OF HEAT SHOCK RESPONSE J. Biol. Chem., September 6, 2002; 277(37): 33641 - 33647. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Cosson, A. Couturier, S. Chabelskaya, D. Kiktev, S. Inge-Vechtomov, M. Philippe, and G. Zhouravleva Poly(A)-Binding Protein Acts in Translation Termination via Eukaryotic Release Factor 3 Interaction and Does Not Influence [PSI+] Propagation Mol. Cell. Biol., May 15, 2002; 22(10): 3301 - 3315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Inal and J. A. Schifferli Complement C2 Receptor Inhibitor Trispanning and the {beta}-Chain of C4 Share a Binding Site for Complement C2 J. Immunol., May 15, 2002; 168(10): 5213 - 5221. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. E. Pace, T. Lebestky, T. Hummel, P. Arnoux, K. Kwan, and L. G. Baum Characterization of a Novel Drosophila melanogaster Galectin. EXPRESSION IN DEVELOPING IMMUNE, NEURAL, AND MUSCLE TISSUES J. Biol. Chem., April 5, 2002; 277(15): 13091 - 13098. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. M. Misenheimer, A. J. Hahr, A. C. Harms, D. S. Annis, and D. F. Mosher Disulfide Connectivity of Recombinant C-terminal Region of Human Thrombospondin 2 J. Biol. Chem., November 30, 2001; 276(49): 45882 - 45887. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. C. Spangenberg, H. B. Lee, J. Li, F. Tan, R. Skidgel, J. R. Wands, and S. Tong A Short Sequence within Domain C of Duck Carboxypeptidase D Is Critical for Duck Hepatitis B Virus Binding and Determines Host Specificity J. Virol., November 15, 2001; 75(22): 10630 - 10642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Facchiano, P. Stiuso, M. L. Chiusano, M. Caraglia, G. Giuberti, M. Marra, A. Abbruzzese, and G. Colonna Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A) Protein Eng. Des. Sel., November 1, 2001; 14(11): 881 - 890. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. T. van Hylckama Vlieg, L. Tang, J. H. Lutje Spelberg, T. Smilda, G. J. Poelarends, T. Bosma, A. E. J. van Merode, M. W. Fraaije, and D. B. Janssen Halohydrin Dehalogenases Are Structurally and Mechanistically Related to Short-Chain Dehydrogenases/Reductases J. Bacteriol., September 1, 2001; 183(17): 5058 - 5066. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Li, B. Kelder, and J. J. Kopchick Identification, Isolation, and Cloning of Growth Hormone (GH)-Inducible Interscapular Brown Adipose Complementary Deoxyribonucleic Acid from GH Antagonist Mice Endocrinology, July 1, 2001; 142(7): 2937 - 2945. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Hasebe, J. Hua, A. Someya, P. Morain, F. Checler, and I. Nagaoka Involvement of cytosolic prolyl endopeptidase in degradation of p40-phox splice variant protein in myeloid cells J. Leukoc. Biol., June 1, 2001; 69(6): 963 - 968. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Karjalainen, A.-J. Waligora-Dupriet, M. Cerquetti, P. Spigaglia, A. Maggioni, P. Mauri, and P. Mastrantonio Molecular and Genomic Analysis of Genes Encoding Surface-Anchored Proteins from Clostridium difficile Infect. Immun., May 1, 2001; 69(5): 3442 - 3446. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Das, A. Dasgupta, S. Sharma, M. Ghosh, T. Sengupta, S. Bandopadhyay, and H. K. Majumder Characterisation of the gene encoding type II DNA topoisomerase from Leishmania donovani: a key molecular target in antileishmanial therapy Nucleic Acids Res., May 1, 2001; 29(9): 1844 - 1851. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A.-J. Waligora, C. Hennequin, P. Mullany, P. Bourlioux, A. Collignon, and T. Karjalainen Characterization of a Cell Surface Protein of Clostridium difficile with Adhesive Properties Infect. Immun., April 1, 2001; 69(4): 2144 - 2153. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. K. Washburn and R. E. Esposito Identification of the Sin3-Binding Site in Ume6 Defines a Two-Step Process for Conversion of Ume6 from a Transcriptional Repressor to an Activator in Yeast Mol. Cell. Biol., March 15, 2001; 21(6): 2057 - 2069. [Abstract] [Full Text]
|
|
|
|
|
|
J. Wu and N. L. Glass Identification of Specificity Determinants and Generation of Alleles with Novel Specificity at the het-c Heterokaryon Incompatibility Locus of Neurospora crassa Mol. Cell. Biol., February 15, 2001; 21(4): 1045 - 1057. [Abstract] [Full Text]
|
|
|
|
|
|
E. H. Cho, R. Alcaraz Jr., R. I. Gumport, and J. F. Gardner Characterization of Bacteriophage Lambda Excisionase Mutants Defective in DNA Binding J. Bacteriol., October 15, 2000; 182(20): 5807 - 5812. [Abstract] [Full Text]
|
|
|
|
 |
|
 J. Zhao, Y. H. Chen, and H. S. Kwan Molecular Cloning, Characterization, and Differential Expression of a Glucoamylase Gene from the Basidiomycetous Fungus Lentinula edodes Appl. Envir. Microbiol., June 1, 2000; 66(6): 2531 - 2535. [Abstract] [Full Text]
|
|
|
|
|
|
K. E. Gregory, J. T. Oxford, Y. Chen, J. E. Gambee, S. P. Gygi, R. Aebersold, P. J. Neame, D. E. Mechling, H. P. Bachinger, and N. P. Morris Structural Organization of Distinct Domains within the Non-collagenous N-terminal Region of Collagen Type XI J. Biol. Chem., April 6, 2000; 275(15): 11498 - 11506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Cosme and E. F. Johnson Engineering Microsomal Cytochrome P450 2C5 to Be a Soluble, Monomeric Enzyme. MUTATIONS THAT ALTER AGGREGATION, PHOSPHOLIPID DEPENDENCE OF CATALYSIS, AND MEMBRANE BINDING J. Biol. Chem., January 28, 2000; 275(4): 2545 - 2553. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. W. Basse, S. Stumpferl, and R. Kahmann Characterization of a Ustilago maydis Gene Specifically Induced during the Biotrophic Phase: Evidence for Negative as Well as Positive Regulation Mol. Cell. Biol., January 1, 2000; 20(1): 329 - 339. [Abstract] [Full Text]
|
|
|
|
 |
|
 V. Perissi, L. M. Staszewski, E. M. McInerney, R. Kurokawa, A. Krones, D. W. Rose, M. H. Lambert, M. V. Milburn, C. K. Glass, and M. G. Rosenfeld Molecular determinants of nuclear receptor-corepressor interaction Genes & Dev., December 15, 1999; 13(24): 3198 - 3208. [Abstract] [Full Text]
|
|
|
|
 |
|
 T. Sakamoto, A. Nishimura, M. Tamaoki, M. Kuba, H. Tanaka, S. Iwahori, and M. Matsuoka The Conserved KNOX Domain Mediates Specificity of Tobacco KNOTTED1-Type Homeodomain Proteins PLANT CELL, August 1, 1999; 11(8): 1419 - 1432. [Abstract] [Full Text]
|
|
|
|
|
|
L. Muller, P. Zhu, M. A. Juliano, L. Juliano, and I. Lindberg A 36-Residue Peptide Contains All of the Information Required for 7B2-mediated Activation of Prohormone Convertase 2 J. Biol. Chem., July 23, 1999; 274(30): 21471 - 21477. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. P. Ellis, H. B. Lukins, P. Nagley, and B. E. Corner Suppression of a Nuclear aep2 Mutation in Saccharomyces cerevisiae by a Base Substitution in the 5'-Untranslated Region of the Mitochondrial oli1 Gene Encoding Subunit 9 of ATP Synthase Genetics, April 1, 1999; 151(4): 1353 - 1363. [Abstract] [Full Text]
|
|
|
|
 |
|
 M. A. Ortiz, J. Light, R. A. Maki, and N. Assa-Munt Mutation analysis of the Pip interaction domain reveals critical residues for protein-protein interactions PNAS, March 16, 1999; 96(6): 2740 - 2745. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Canaves and M. Montal Assembly of a Ternary Complex by the Predicted Minimal Coiled-coil-forming Domains of Syntaxin, SNAP-25, and Synaptobrevin. A CIRCULAR DICHROISM STUDY J. Biol. Chem., December 18, 1998; 273(51): 34214 - 34221. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Halpert, T. L. Domanski, O. Adali, C. P. Biagini, J. Cosme, E. A. Dierks, E. F. Johnson, J. P. Jones, P. O. de Montellano, R. M. Philpot, et al. Structure-Function of Cytochromes P450 and Flavin-Containing Monooxygenases. Implications for Drug Metabolism Drug Metab. Dispos., December 1, 1998; 26(12): 1223 - 1231. [Abstract] [Full Text]
|
|
|
|
|
|
J. A. Lopez, R. Bustos, C. Orvell, M. Berois, J. Arbiza, B. Garcia-Barreno, and J. A. Melero Antigenic Structure of Human Respiratory Syncytial Virus Fusion Glycoprotein J. Virol., August 1, 1998; 72(8): 6922 - 6928. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Brooun, J. Bell, T. Freitas, R. W. Larsen, and M. Alam An Archaeal Aerotaxis Transducer Combines Subunit I Core Structures of Eukaryotic Cytochrome c Oxidase and Eubacterial Methyl-Accepting Chemotaxis Proteins J. Bacteriol., April 1, 1998; 180(7): 1642 - 1646. [Abstract] [Full Text]
|
|
|
|
|
|
I. Casin, F. Bordon, P. Bertin, A. Coutrot, I. Podglajen, R. Brasseur, and E. Collatz Aminoglycoside 6'-N-Acetyltransferase Variants of the Ib Type with Altered Substrate Profile in Clinical Isolates of Enterobacter cloacae and Citrobacter freundii Antimicrob. Agents Chemother., February 1, 1998; 42(2): 209 - 215. [Abstract] [Full Text]
|
|
|
|
|
|
S. A. Filppula, A. I. Yagi, S. H. Kilpelainen, D. Novikov, D. R. FitzPatrick, M. Vihinen, D. Valle, and J. K. Hiltunen Delta 3,5-Delta 2,4-Dienoyl-CoA Isomerase from Rat Liver. MOLECULAR CHARACTERIZATION J. Biol. Chem., January 2, 1998; 273(1): 349 - 355. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Seidel, K. Adermann, T. Schindler, A. Ejchart, R. Jaenicke, W.-G. Forssmann, and P. Rosch Solution Structure of Porcine Delta Sleep-inducing Peptide Immunoreactive Peptide A Homolog of the Shortsighted Gene Product J. Biol. Chem., December 5, 1997; 272(49): 30918 - 30927. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A. Ascoli, K. X. Luu, J. L. Olds, T. J. Nelson, P. A. Gusev, C. Bertucci, E. Bramanti, A. Raffaelli, P. Salvadori, and D. L. Alkon Secondary Structure and Ca2+-induced Conformational Change of Calexcitin, a Learning-associated Protein J. Biol. Chem., October 3, 1997; 272(40): 24771 - 24779. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Rink, M. Fennema, M. Smids, U. Dehmel, and D. B. Janssen Primary Structure and Catalytic Mechanism of the Epoxide Hydrolase from Agrobacterium radiobacter AD1 J. Biol. Chem., June 6, 1997; 272(23): 14650 - 14657. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Gerken, C. L. Owens, and M. Pasumarthy Determination of the Site-specific O-Glycosylation Pattern of the Porcine Submaxillary Mucin Tandem Repeat Glycopeptide. MODEL PROPOSED FOR THE POLYPEPTIDE:GalNAc TRANSFERASE PEPTIDE BINDING SITE J. Biol. Chem., April 11, 1997; 272(15): 9709 - 9719. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S Zaffran, M Astier, D Gratecos, and M Semeriva The held out wings (how) Drosophila gene encodes a putative RNA-binding protein involved in the control of muscular and cardiac activity Development, January 5, 1997; 124(10): 2087 - 2098. [Abstract] [PDF]
|
|
|
|
|
|
M. T. Washington, A. H. Rosenberg, K. Griffin, F. W. Studier, and S. S. Patel Biochemical Analysis of Mutant T7 Primase/Helicase Proteins Defective in DNA Binding, Nucleotide Hydrolysis, and the Coupling of Hydrolysis with DNA Unwinding J. Biol. Chem., October 25, 1996; 271(43): 26825 - 26834. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Puzon-McLaughlin and Y. Takada Critical Residues for Ligand Binding in an I Domain-like Structure of the Integrin beta 1 Subunit J. Biol. Chem., August 23, 1996; 271(34): 20438 - 20443. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Faber, A. Lindemann, H. Sticht, A. Ejchart, A. Kungl, M. Susani, R. W. Frank, D. Kraft, M. Breitenbach, and P. Rosch Secondary Structure and Tertiary Fold of the Birch Pollen Allergen Bet v 1in Solution J. Biol. Chem., August 9, 1996; 271(32): 19243 - 19250. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. F. McGinnity, B. Devreese, S. Prazeres, J. Van Beeumen, I. Moura, J. J. G. Moura, and G. W. Pettigrew A Single Histidine Is Required for Activity of Cytochrome c Peroxidase from Paracoccus denitrificans J. Biol. Chem., May 10, 1996; 271(19): 11126 - 11133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Seroz, C. Perez, E. Bergmann, J. Bradsher, and J.-M. Egly p44/SSL1, the Regulatory Subunit of the XPD/RAD3 Helicase, Plays a Crucial Role in the Transcriptional Activity of TFIIH J. Biol. Chem., October 20, 2000; 275(43): 33260 - 33266. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Mayr, K. Richter, H. Lilie, and J. Buchner Cpr6 and Cpr7, Two Closely Related Hsp90-associated Immunophilins from Saccharomyces cerevisiae, Differ in Their Functional Properties J. Biol. Chem., October 27, 2000; 275(44): 34140 - 34146. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Bishop and P. Woodman TSG101/Mammalian VPS23 and Mammalian VPS28 Interact Directly and Are Recruited to VPS4-induced Endosomes J. Biol. Chem., April 6, 2001; 276(15): 11735 - 11742. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. J. Topol, J. McCarthy, S. Gabriel, D. J. Moliterno, W. J. Rogers, L. K. Newby, M. Freedman, J. Metivier, R. Cannata, C. J. O'Donnell, et al. Single Nucleotide Polymorphisms in Multiple Novel Thrombospondin Genes May Be Associated With Familial Premature Myocardial Infarction Circulation, November 27, 2001; 104(22): 2641 - 2644. [Abstract] [Full Text] [PDF]
|
|