PHD-an automatic mail server for protein secondary structure prediction
EMBL, Meyerhofstrasse I, D-69117 Heidelberg, Germany
By the middle of 1993, >30 000 protein sequences had been listed. For 1000 of these, the three-dimensional (tertiary) structure has been experimentally solved. Another 7000 can be modelled by homology. For the remaining 21 000 sequences, secondary structure prediction provides a rough estimate of structural features. Predictions in three states range between 35% (random) and 88% (homology modelling) overall accuracy. Using information about evolutionary conservation as contained in multiple sequence alignments, the secondary structure of 4700 protein sequences was predicted by the automatic e-mail server PHD. For proteins with at least one known homologue, the method has an expected overall three-state accuracy of 71.4% for proteins with at least one known homologue (e on 126 unique protein chains).
Received on July 27, 1993; accepted on September 30, 1993
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M. Hartung and B. Kisters-Woike Cre Mutants with Altered DNA Binding Properties J. Biol. Chem., September 4, 1998; 273(36): 22884 - 22891. [Abstract] [Full Text] [PDF]
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A. G. Ladurner, L. S. Itzhaki, V. Daggett, and A. R. Fersht Synergy between simulation and experiment in describing the energy landscape of protein folding PNAS, July 21, 1998; 95(15): 8473 - 8478. [Abstract] [Full Text] [PDF]
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G. Zhang and S. A. Darst Structure of the Escherichia coli RNA Polymerase  Subunit Amino-Terminal DomainScience, July 10, 1998; 281(5374): 262 - 266. [Abstract] [Full Text]
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K. E. Reed, A. E. Gorbalenya, and C. M. Rice The NS5A/NS5 Proteins of Viruses from Three Genera of the Family Flaviviridae Are Phosphorylated by Associated Serine/Threonine Kinases J. Virol., July 1, 1998; 72(7): 6199 - 6206. [Abstract] [Full Text] [PDF]
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R. C. Bugos, A. D. Hieber, and H. Y. Yamamoto Xanthophyll Cycle Enzymes Are Members of the Lipocalin Family, the First Identified from Plants J. Biol. Chem., June 19, 1998; 273(25): 15321 - 15324. [Abstract] [Full Text] [PDF]
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J. Peng, N. F. Marshall, and D. H. Price Identification of a Cyclin Subunit Required for the Function of Drosophila P-TEFb J. Biol. Chem., May 29, 1998; 273(22): 13855 - 13860. [Abstract] [Full Text] [PDF]
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J. Schultz, F. Milpetz, P. Bork, and C. P. Ponting SMART, a simple modular architecture research tool: Identification of signaling domains PNAS, May 26, 1998; 95(11): 5857 - 5864. [Abstract] [Full Text] [PDF]
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L. Aravind, E. V. Koonin;, M. Dangl, A. Lusser, G. Brosch, A. Loidl, H. Haas, and P. Loidl; Second Family of Histone Deacetylases Science, May 22, 1998; 280(5367): 1167a - 1167. [Full Text]
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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]
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J. Zheng, R.-H. Chen, S. Corblan-Garcia, S. M. Cahill, D. Bar-Sagi, and D. Cowburn The Solution Structure of the Pleckstrin Homology Domain of Human SOS1. A POSSIBLE STRUCTURAL ROLE FOR THE SEQUENTIAL ASSOCIATION OF DIFFUSE B CELL LYMPHOMA AND PLECKSTRIN HOMOLOGY DOMAINS J. Biol. Chem., November 28, 1997; 272(48): 30340 - 30344. [Abstract] [Full Text] [PDF]
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R. C. Aguilar, H. Ohno, K. W. Roche, and J. S. Bonifacino Functional Domain Mapping of the Clathrin-associated Adaptor Medium Chains µ1 and µ2 J. Biol. Chem., October 24, 1997; 272(43): 27160 - 27166. [Abstract] [Full Text] [PDF]
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M. D. Sutton and J. M. Kaguni Threonine 435 of Escherichia coli DnaA Protein Confers Sequence-specific DNA Binding Activity J. Biol. Chem., September 12, 1997; 272(37): 23017 - 23024. [Abstract] [Full Text] [PDF]
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J. Merilainen, V.-P. Lehto, and V.-M. Wasenius FAP52, a Novel, SH3 Domain-containing Focal Adhesion Protein J. Biol. Chem., September 12, 1997; 272(37): 23278 - 23284. [Abstract] [Full Text] [PDF]
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L. Zhang and R. G. Birch The gene for albicidin detoxification from Pantoea dispersa encodes an esterase and attenuates pathogenicity of Xanthomonas albilineans to sugarcane PNAS, September 2, 1997; 94(18): 9984 - 9989. [Abstract] [Full Text] [PDF]
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L. Franzoni, G. Nicastro, T. A. Pertinhez, M. Tato, C. R. Nakaie, A. C.M. Paiva, S. Schreier, and A. Spisni Structure of the C-terminal Fragment 300-320 of the Rat Angiotensin II AT1A Receptor and Its Relevance with Respect to G-Protein Coupling J. Biol. Chem., April 11, 1997; 272(15): 9734 - 9741. [Abstract] [Full Text] [PDF]
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R. A. Ridsdale, D. R. Beniac, T. A. Tompkins, M. A. Moscarello, and G. Harauz Three-dimensional Structure of Myelin Basic Protein. II. MOLECULAR MODELING AND CONSIDERATIONS OF PREDICTED STRUCTURES IN MULTIPLE SCLEROSIS J. Biol. Chem., February 14, 1997; 272(7): 4269 - 4275. [Abstract] [Full Text] [PDF]
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A. N. Hodder, P. E. Crewther, M. L.S.M. Matthew, G. E. Reid, R. L. Moritz, R. J. Simpson, and R. F. Anders The Disulfide Bond Structure of Plasmodium Apical Membrane Antigen-1 J. Biol. Chem., November 15, 1996; 271(46): 29446 - 29452. [Abstract] [Full Text] [PDF]
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B. C. Krovat and M. F. Jantsch Comparative Mutational Analysis of the Double-stranded RNA Binding Domains of Xenopus laevis RNA-binding Protein A J. Biol. Chem., November 8, 1996; 271(45): 28112 - 28119. [Abstract] [Full Text] [PDF]
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L. C. Lee, J. J. Hunter, A. Mujeeb, C. Turck, and T. G. Parslow Evidence for alpha -Helical Conformation of an Essential N-terminal Region in the Human Bcl2 Protein J. Biol. Chem., September 20, 1996; 271(38): 23284 - 23288. [Abstract] [Full Text] [PDF]
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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]
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W. L. Nowatzke and J. P. Richardson Characterization of an Unusual Rho Factor from the High G + C Gram-positive Bacterium Micrococcus luteus J. Biol. Chem., January 12, 1996; 271(2): 742 - 747. [Abstract] [Full Text] [PDF]
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