Predicting protein crystallization propensity from protein sequence
暂无分享,去创建一个
[1] Stephen K. Burley,et al. High-throughput Limited Proteolysis/Mass Spectrometry for Protein Domain Elucidation , 2005, Journal of Structural and Functional Genomics.
[2] Mark Gerstein,et al. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics , 2001, Nucleic Acids Res..
[3] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[4] J. Celis,et al. Reference points for comparisons of two‐dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions , 1994, Electrophoresis.
[5] Minoru Kanehisa,et al. AAindex: amino acid index database, progress report 2008 , 2007, Nucleic Acids Res..
[6] S. Rackovsky,et al. Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids , 1982 .
[7] Lukasz Kurgan,et al. Prediction of protein crystallization using collocation of amino acid pairs. , 2007, Biochemical and biophysical research communications.
[8] Sean R. Eddy,et al. Multiple Alignment Using Hidden Markov Models , 1995, ISMB.
[9] T. Sejnowski,et al. Predicting the secondary structure of globular proteins using neural network models. , 1988, Journal of molecular biology.
[10] Mark A. Girolami,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btn055 Sequence analysis ParCrys: a Parzen window density estimation approach , 2022 .
[11] Dmitrij Frishman,et al. Will my protein crystallize? A sequence‐based predictor , 2005, Proteins.
[12] B. Matthews. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.
[13] Carol S. Giometti,et al. GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes , 2004, Nucleic Acids Res..
[14] A Elofsson,et al. Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale. , 1999, Journal of molecular biology.
[15] A. Dong,et al. In situ proteolysis for protein crystallization and structure determination , 2007, Nature Methods.
[16] J. Richardson,et al. Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.
[17] V. Muñoz,et al. Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales , 1994 .
[18] Sean R. Eddy,et al. Maximum Discrimination Hidden Markov Models of Sequence Consensus , 1995, J. Comput. Biol..
[19] Youngchang Kim,et al. Large-scale evaluation of protein reductive methylation for improving protein crystallization , 2008, Nature Methods.
[20] Erik L. L. Sonnhammer,et al. Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..
[21] A. Joachimiak,et al. Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes. , 2005, Journal of molecular biology.
[22] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[23] David Eisenberg,et al. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants , 2007, Protein science : a publication of the Protein Society.
[24] H. Scheraga,et al. Statistical mechanical treatment of protein conformation. II. A three-state model for specific-sequence copolymers of amino acids. , 1976, Macromolecules.
[25] Teuvo Kohonen,et al. Self-organized formation of topologically correct feature maps , 2004, Biological Cybernetics.
[26] C. Koth,et al. Use of limited proteolysis to identify protein domains suitable for structural analysis. , 2003, Methods in enzymology.
[27] Christine A Orengo,et al. Target selection for structural genomics: an overview. , 2008, Methods in molecular biology.
[28] Geoffrey J Barton,et al. A normalised scale for structural genomics target ranking: The OB‐Score , 2006, FEBS letters.
[29] H. Scheraga,et al. Statistical mechanical treatment of protein conformation. 5. A multistate model for specific-sequence copolymers of amino acids. , 1977, Macromolecules.
[30] P Argos,et al. Protein secondary structure. Studies on the limits of prediction accuracy. , 2009, International journal of peptide and protein research.
[31] S. Rackovsky,et al. Differential Geometry and Polymer Conformation. 1. Comparison of Protein Conformations1a,b , 1978 .
[32] Leszek Rychlewski,et al. The challenge of protein structure determination—lessons from structural genomics , 2007, Protein science : a publication of the Protein Society.
[33] S. Eddy. Hidden Markov models. , 1996, Current opinion in structural biology.
[34] Rebecca Page,et al. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. , 2004, Journal of molecular biology.
[35] P. Y. Chou,et al. Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .
[36] H. Szurmant,et al. Extracytoplasmic PAS-Like Domains Are Common in Signal Transduction Proteins , 2009, Journal of bacteriology.
[37] Bernard F. Buxton,et al. The DISOPRED server for the prediction of protein disorder , 2004, Bioinform..
[38] Christopher J. Oldfield,et al. Addressing the intrinsic disorder bottleneck in structural proteomics , 2005, Proteins.
[39] Piero Fariselli,et al. A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins , 2002, ISMB.
[40] C. Chothia. Structural invariants in protein folding , 1975, Nature.
[41] Vladimir Vapnik,et al. An overview of statistical learning theory , 1999, IEEE Trans. Neural Networks.
[42] B. Rost,et al. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data , 2009, Nature Biotechnology.
[43] F. Collart,et al. A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. , 2002, Protein expression and purification.
[44] Mark Gerstein,et al. SPINE 2: a system for collaborative structural proteomics within a federated database framework. , 2003, Nucleic acids research.
[45] P. Ponnuswamy,et al. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. , 1980, Biochimica et biophysica acta.
[46] G von Heijne,et al. A turn propensity scale for transmembrane helices. , 1999, Journal of molecular biology.
[47] Minoru Kanehisa,et al. AAindex: Amino Acid index database , 2000, Nucleic Acids Res..
[48] Leszek Rychlewski,et al. XtalPred: a web server for prediction of protein crystallizability , 2007, Bioinform..