Tools for Protein Technologies

[1]  K. Gevaert,et al.  Protein identification methods in proteomics , 2000, Electrophoresis.

[2]  R. Aebersold,et al.  Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. , 2000, Analytical chemistry.

[3]  T K Attwood,et al.  The quest to deduce protein function from sequence: the role of pattern databases. , 2000, The international journal of biochemistry & cell biology.

[4]  N. Blom,et al.  Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. , 1999, Journal of molecular biology.

[5]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[6]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[7]  P F Lemkin,et al.  Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database , 1999, Molecular biotechnology.

[8]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[9]  Shmuel Pietrokovski,et al.  Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations , 1999, Bioinform..

[10]  P Argos,et al.  DOMO: a new database of aligned protein domains. , 1998, Trends in biochemical sciences.

[11]  Morten Østergaard,et al.  Human and mouse proteomic databases: novel resources in the protein universe , 1998, FEBS letters.

[12]  C Geourjon,et al.  Protein structure prediction. Implications for the biologist. , 1997, Biochimie.

[13]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[14]  B. Rost,et al.  Protein fold recognition by prediction-based threading. , 1997, Journal of molecular biology.

[15]  J. M. Levin,et al.  Exploring the limits of nearest neighbour secondary structure prediction. , 1997, Protein engineering.

[16]  M Wilm,et al.  Peptide Sequencing by Mass Spectrometry for Homology Searches and Cloning of Genes , 1997, Journal of protein chemistry.

[17]  J. Yates,et al.  Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides , 1996, Journal of the American Society for Mass Spectrometry.

[18]  S. Rogers,et al.  PEST sequences and regulation by proteolysis. , 1996, Trends in biochemical sciences.

[19]  G. Barton,et al.  Protein fold recognition by mapping predicted secondary structures. , 1996, Journal of molecular biology.

[20]  Thomas Madej,et al.  Threading analysis suggests that the obese gene product may be a helical cytokine , 1995, FEBS letters.

[21]  B. Rost,et al.  Transmembrane helices predicted at 95% accuracy , 1995, Protein science : a publication of the Protein Society.

[22]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[23]  T K Attwood,et al.  OWL--a non-redundant composite protein sequence database. , 1994, Nucleic acids research.

[24]  T. Hunkapiller,et al.  Peptide mass maps: a highly informative approach to protein identification. , 1993, Analytical biochemistry.

[25]  P Bork,et al.  Evolutionarily mobile modules in proteins. , 1993, Scientific American.

[26]  P. Højrup,et al.  Rapid identification of proteins by peptide-mass fingerprinting , 1993, Current Biology.

[27]  P. Højrup,et al.  Use of mass spectrometric molecular weight information to identify proteins in sequence databases. , 1993, Biological mass spectrometry.

[28]  S. Bryant,et al.  An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.

[29]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[30]  M Kanehisa,et al.  Construction of a dictionary of sequence motifs that characterize groups of related proteins , 1992, Protein engineering.

[31]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[32]  M. Sippl,et al.  Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations , 1992, Proteins.

[33]  David L. Wilkinson,et al.  Predicting the Solubility of Recombinant Proteins in Escherichia coli , 1991, Bio/Technology.

[34]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[35]  T. Sejnowski,et al.  Predicting the secondary structure of globular proteins using neural network models. , 1988, Journal of molecular biology.

[36]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[37]  A. D. McLachlan,et al.  Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Varshavsky,et al.  In vivo half-life of a protein is a function of its amino-terminal residue. , 1986, Science.

[39]  Barry Robson,et al.  An algorithm for secondary structure determination in proteins based on sequence similarity , 1986, FEBS letters.

[40]  M. Karplus,et al.  An analysis of incorrectly folded protein models. Implications for structure predictions. , 1984, Journal of molecular biology.

[41]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[42]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[43]  P F Lemkin,et al.  Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. , 1980, Clinical chemistry.

[44]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[45]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[46]  F. Sanger,et al.  Nucleotide sequence of bacteriophage φX174 DNA , 1977, Nature.

[47]  C. Chothia.  The nature of the accessible and buried surfaces in proteins. , 1976, Journal of molecular biology.

[48]  V. Lim.  Algorithms for prediction of α-helical and β-structural regions in globular proteins , 1974 .

[49]  P. Y. Chou,et al.  Prediction of protein conformation. , 1974, Biochemistry.

[50]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[51]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[52]  H. F. Fisher,et al.  A LIMITING LAW RELATING THE SIZE AND SHAPE OF PROTEIN MOLECULES TO THEIR COMPOSITION. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Peter B. McGarvey,et al.  The Protein Information Resource (PIR) , 2000, Nucleic Acids Res..

[54]  Ron D. Appel,et al.  The 1999 SWISS-2DPAGE database update , 2000, Nucleic Acids Res..

[55]  J R Yates,et al.  Mass spectrometry. From genomics to proteomics. , 2000, Trends in genetics : TIG.

[56]  W R Pearson,et al.  Flexible sequence similarity searching with the FASTA3 program package. , 2000, Methods in molecular biology.

[57]  David S. Wishart,et al.  PepTool™ and GeneTool™: , 2000 .

[58]  Jérôme Gouzy,et al.  ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons , 2000, Nucleic Acids Res..

[59]  J. Venter,et al.  Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium. , 2000, Annual review of pharmacology and toxicology.

[60]  Terri K. Attwood,et al.  PRINTS prepares for the new millennium , 1999, Nucleic Acids Res..

[61]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[62]  R D Appel,et al.  Melanie II – a third‐generation software package for analysis of two‐dimensional electrophoresis images: II. Algorithms , 1997, Electrophoresis.

[63]  B. Rost.  PHD: predicting one-dimensional protein structure by profile-based neural networks. , 1996, Methods in enzymology.

[64]  A. Lupas.  Prediction and analysis of coiled-coil structures. , 1996, Methods in enzymology.

[65]  M. Kanehisa,et al.  Fragment peptide library for classification and functional prediction of proteins , 1990, Proteins.

[66]  D. Hochstrasser,et al.  Automatic classification of two‐dimensional gel electrophoresis pictures by heuristic clustering analysis: A step toward machine learning , 1988, Electrophoresis.

[67]  T. Steitz,et al.  Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. , 1986, Annual review of biophysics and biophysical chemistry.

[68]  A. Zamyatnin,et al.  Protein volume in solution. , 1972, Progress in biophysics and molecular biology.

[69]  H Nielsen,et al.  Machine learning approaches for the prediction of signal peptides and other protein sorting signals. , 1999, Protein engineering.