Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases
暂无分享,去创建一个
Andrés Moya | Ricardo Futami | Carlos Llorens | Gabriel Renaud | G. Renaud | A. Moya | C. Lloréns | R. Futami | Gabriel Renaud
[1] T. L. Blundell,et al. Structural evidence for gene duplication in the evolution of the acid proteases , 1978, Nature.
[2] J. Thornton,et al. A revised set of potentials for β‐turn formation in proteins , 1994 .
[3] K. Schweimer,et al. The solution structure of the simian foamy virus protease reveals a monomeric protein. , 2008, Journal of molecular biology.
[4] T. D. Schneider,et al. Information content of binding sites on nucleotide sequences. , 1986, Journal of molecular biology.
[5] D. Fass,et al. Ddi1, a eukaryotic protein with the retroviral protease fold. , 2006, Journal of molecular biology.
[6] B. L. Sibanda,et al. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. , 1989, Journal of molecular biology.
[7] C E Shannon,et al. The mathematical theory of communication. 1963. , 1997, M.D. computing : computers in medical practice.
[8] G. Rose,et al. Turns in peptides and proteins. , 1985, Advances in protein chemistry.
[9] Richard A. Goldstein,et al. Probabilistic reconstruction of ancestral protein sequences , 1996, Journal of Molecular Evolution.
[10] C. E. SHANNON,et al. A mathematical theory of communication , 1948, MOCO.
[11] P. Brindley,et al. The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements , 2005, BMC Evolutionary Biology.
[12] T. D. Schneider,et al. Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.
[13] C. Venkatachalam. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units , 1968, Biopolymers.
[14] Sang Joon Kim,et al. A Mathematical Theory of Communication , 2006 .
[15] D. Lipman,et al. National Center for Biotechnology Information , 2019, Springer Reference Medizin.
[16] Liam J. McGuffin,et al. The PSIPRED protein structure prediction server , 2000, Bioinform..
[17] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[18] A. Moya,et al. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis , 2008, BMC Evolutionary Biology.
[19] Manuel C. Peitsch,et al. SWISS-MODEL: an automated protein homology-modeling server , 2003, Nucleic Acids Res..
[20] M. Jaskólski,et al. Molecular replacement with pseudosymmetry and model dissimilarity: a case study. , 2006, Acta crystallographica. Section D, Biological crystallography.
[21] A Wlodawer,et al. Structural and biochemical studies of retroviral proteases. , 2000, Biochimica et biophysica acta.
[22] Alan M. Lambowitz,et al. Mobile DNA III , 2002 .
[23] Fred R. McMorris,et al. Consensusn-trees , 1981 .
[24] R. Shamir,et al. A fast algorithm for joint reconstruction of ancestral amino acid sequences. , 2000, Molecular biology and evolution.
[25] D. M. Krylov,et al. Correspondence A novel family of predicted retroviral-like aspartyl proteases with a possible key role in eukaryotic cell cycle control , 2001, Current Biology.
[26] M. Tristem,et al. The Evolution, Distribution and Diversity of Endogenous Retroviruses , 2003, Virus Genes.
[27] T. D. Schneider,et al. Consensus sequence Zen. , 2002, Applied bioinformatics.
[28] Andrés Moya,et al. The Gypsy Database (GyDB) of mobile genetic elements , 2008, Nucleic Acids Res..
[29] Neil D. Rawlings,et al. MEROPS: the peptidase database , 2009, Nucleic Acids Res..
[30] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[31] N. Andreeva. A consensus template for the aspartic proteinase fold. , 1991, Advances in experimental medicine and biology.
[32] D. Mager,et al. Endogenous Human Retroviruses , 1994 .
[33] Tom Blundell,et al. The active site of aspartic proteinases , 1991, FEBS letters.
[34] William R. Taylor,et al. A structural model for the retroviral proteases , 1987, Nature.
[35] A. Alix,et al. High accuracy prediction of β‐turns and their types using propensities and multiple alignments , 2005 .
[36] J. Thornton,et al. A revised set of potentials for beta-turn formation in proteins. , 1994, Protein science : a publication of the Protein Society.
[37] Colin N. Dewey,et al. Initial sequencing and comparative analysis of the mouse genome. , 2002 .
[38] J. Jurka,et al. A universal classification of eukaryotic transposable elements implemented in Repbase , 2008, Nature Reviews Genetics.
[39] M. Jaskólski,et al. Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[40] I. Weber. Structural alignment of retroviral protease sequences. , 1989, Gene.
[41] M. O. Dayhoff,et al. Atlas of protein sequence and structure , 1965 .
[42] M. Nei,et al. A new method of inference of ancestral nucleotide and amino acid sequences. , 1995, Genetics.
[43] X. Puente,et al. Human and mouse proteases: a comparative genomic approach , 2003, Nature Reviews Genetics.
[44] W. Fitch. Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .
[45] J S Fruton,et al. The mechanism of the catalytic action of pepsin and related acid proteinases. , 2006, Advances in enzymology and related areas of molecular biology.
[46] Viktor Hornak,et al. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. , 2006, Journal of the American Chemical Society.
[47] M. Tristem,et al. Evolution and Distribution of Class II-Related Endogenous Retroviruses , 2005, Journal of Virology.
[48] J. Aldrich. R.A. Fisher and the making of maximum likelihood 1912-1922 , 1997 .
[49] B. Dunn. Overview of Pepsin-like Aspartic Peptidases , 2003 .
[50] J. Louis,et al. Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. , 1998, Biochemistry.
[51] P. Meisel. Margaret O. Dayhoff: Atlas of Protein Sequence and Structure 1969 (Volume 4) XXIV u. 361 S., 21 Ausklapptafeln, 68 Abb. und zahlreiche Tabellen. National Biomedical Research Foundation, Silver Spring/Maryland 1969. Preis $ 12,50 , 1971 .
[52] M. Donovan,et al. Identification and characterization of a novel retroviral-like aspartic protease specifically expressed in human epidermis. , 2005, The Journal of investigative dermatology.
[53] M. Freeling,et al. A low copy number, copia‐like transposon in maize. , 1985, The EMBO journal.
[54] N. Bowen,et al. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. , 1999, Genome research.
[55] J. Thompson,et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.
[56] T. Eickbush,et al. Origins and Evolution of Retrotransposons , 2002 .
[57] A. Oskooi. Molecular Evolution and Phylogenetics , 2008 .
[58] J. Kapfhammer,et al. Differential ligand-dependent protein-protein interactions between nuclear receptors and a neuronal-specific cofactor. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[59] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[60] T. Matsui,et al. Mouse Homologue of Skin-specific Retroviral-like Aspartic Protease Involved in Wrinkle Formation* , 2006, Journal of Biological Chemistry.