Technologies of protein interactomics: A review
暂无分享,去创建一个
A. I. Archakov | A. Ivanov | A. Archakov | V. Zgoda | A. S. Ivanov | V. G. Zgoda | Alexis S. Ivanov | Victor G. Zgoda | Alexander I. Archakov | V. G. Zgoda
[1] Gary D Bader,et al. Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.
[2] K. N. Chandrika,et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets , 2006, Nature Genetics.
[3] Anton J. Enright,et al. Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.
[4] M. Vidal,et al. Prospects for drug screening using the reverse two-hybrid system. , 1999, Trends in biotechnology.
[5] J. Acker,et al. Eukaryotic GST fusion vector for the study of protein-protein associations in vivo: application to interaction of ATFa with Jun and Fos. , 1995, BioTechniques.
[6] D. Eisenberg,et al. A combined algorithm for genome-wide prediction of protein function , 1999, Nature.
[7] Jason H. Moore,et al. Role for protein–protein interaction databases in human genetics , 2009, Expert review of proteomics.
[8] A. Lisitsa,et al. Biosensor analysis of the interaction of potential dimerization inhibitors with HIV-1 protease , 2009, Biomeditsinskaia khimiia.
[9] S. Fields,et al. A novel genetic system to detect proteinprotein interactions , 1989, Nature.
[10] P. Uetz. Two-hybrid arrays. , 2002, Current opinion in chemical biology.
[11] Joachim Klose,et al. Two‐dimensional electrophoresis of proteins: An updated protocol and implications for a functional analysis of the genome , 1995, Electrophoresis.
[12] A. Grigoriev. On the number of protein-protein interactions in the yeast proteome. , 2003, Nucleic acids research.
[13] Axel Facius,et al. Bioinformatics challenges in proteomics. , 2005, Combinatorial chemistry & high throughput screening.
[14] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[15] See-Kiong Ng,et al. A correlated motif approach for finding short linear motifs from protein interaction networks , 2006, BMC Bioinformatics.
[16] Jean-Loup Faulon,et al. Predicting protein-protein interactions using signature products , 2005, Bioinform..
[17] B. Séraphin,et al. A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.
[18] Hui Lu,et al. MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading , 2002, Proteins.
[19] A. Sickmann,et al. Identification and isolation of Dictyostelium microtubule-associated protein interactors by tandem affinity purification. , 2006, European journal of cell biology.
[20] R. Finn,et al. Identifying Protein Domains with the Pfam Database , 2003, Current protocols in bioinformatics.
[21] B. Balgley,et al. Comprehensive yeast proteome analysis using a capillary isoelectric focusing‐based multidimensional separation platform coupled with ESI‐MS/MS , 2007, Proteomics.
[22] E. Sprinzak,et al. Correlated sequence-signatures as markers of protein-protein interaction. , 2001, Journal of molecular biology.
[23] Weiwen Zhang,et al. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. , 2010, Microbiology.
[24] Albert Chan,et al. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs , 2006, BMC Bioinformatics.
[25] H. Schägger,et al. Native electrophoretic techniques to identify protein–protein interactions , 2009, Proteomics.
[26] G. Church,et al. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae , 2001, Nature Genetics.
[27] Baldomero Oliva,et al. Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships , 2005, Bioinform..
[28] A. Bauch,et al. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells , 2006, Nature Methods.
[29] Patrick Aloy,et al. Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[30] A. Sytkowski,et al. Variability in the immunodetection of His-tagged recombinant proteins. , 2006, Analytical biochemistry.
[31] S. Fields,et al. Protein-protein interactions: methods for detection and analysis , 1995, Microbiological reviews.
[32] R. Nelson,et al. Design and use of multi‐affinity surfaces in biomolecular interaction analysis–mass spectrometry (BIA/MS): a step toward the design of SPR/MS arrays , 2003, Journal of molecular recognition : JMR.
[33] R. Durbin,et al. Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.
[34] R. Gentz,et al. 6xHis-Ni-NTA chromatography as a superior technique in recombinant protein expression/purification. , 1994, Methods in molecular biology.
[35] Robert B. Russell,et al. InterPreTS: protein Interaction Prediction through Tertiary Structure , 2003, Bioinform..
[36] A. Lisitsa,et al. Biospecific irreversible fishing coupled with atomic force microscopy for detection of extremely low‐abundant proteins , 2009, Proteomics.
[37] William Stafford Noble,et al. Predicting Co-Complexed Protein Pairs from Heterogeneous Data , 2008, PLoS Comput. Biol..
[38] Andrew J Link,et al. Tandem affinity purification and identification of protein complex components. , 2004, Methods.
[39] E. Marcotte,et al. Computational genetics: finding protein function by nonhomology methods. , 2000, Current opinion in structural biology.
[40] David A. Gough,et al. Predicting protein-protein interactions from primary structure , 2001, Bioinform..
[41] P. O’Farrell. High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.
[42] A. Heck,et al. Surface plasmon resonance mass spectrometry in proteomics , 2008, Expert review of proteomics.
[43] Liisa Holm,et al. Evaluation of different domain-based methods in protein interaction prediction. , 2009, Biochemical and biophysical research communications.
[44] E. Enerly,et al. Conservation of gene order, structure and sequence between three closely linked genes in Drosophila melanogaster and Drosophila virilis. , 2002, Gene.
[45] D. F. Waugh,et al. Protein-protein interactions. , 1954, Advances in protein chemistry.
[46] Minghua Deng,et al. Inferring Domain–Domain Interactions From Protein–Protein Interactions , 2002 .
[47] S. Masters,et al. Co-immunoprecipitation from transfected cells. , 2004, Methods in molecular biology.
[48] Shoshana J Wodak,et al. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. , 2004, Current opinion in structural biology.
[49] James R. Knight,et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.
[50] Jos Buijs,et al. Optimizing the surface plasmon resonance/mass spectrometry interface for functional proteomics applications: How to avoid and utilize nonspecific adsorption , 2006, Proteomics.
[51] V. Zgoda,et al. Fluorescent immunoprecipitation analysis of cell surface proteins: a methodology compatible with mass-spectrometry. , 2007, Journal of immunological methods.
[52] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[53] H. Lehrach,et al. A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.
[54] Sara Linse,et al. Methods for the detection and analysis of protein–protein interactions , 2007, Proteomics.
[55] John R Yates,et al. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). , 2009, Journal of proteome research.
[56] P. Lewi,et al. Protein–protein interactions: mechanisms and modification by drugs , 2002, Journal of molecular recognition : JMR.
[57] D G Myszka,et al. Advances in surface plasmon resonance biosensor analysis. , 2000, Current opinion in biotechnology.
[58] H. Schägger,et al. Features and applications of blue‐native and clear‐native electrophoresis , 2008, Proteomics.
[59] Andrey Lisitsa,et al. Protein-protein Interactions as New Targets for Drug Design: Virtual and Experimental Approaches , 2007, J. Bioinform. Comput. Biol..
[60] B. Séraphin,et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.
[61] Elisabetta Gianazza,et al. Protein stains for proteomic applications: Which, when, why? , 2006, Proteomics.
[62] Steven Fletcher,et al. Protein-protein interaction inhibitors: small molecules from screening techniques. , 2007, Current topics in medicinal chemistry.
[63] A. Archakov. Inhibitors of Protein-Protein Interactions as Potential Drugs , 2007 .
[64] Mark Gerstein,et al. Getting Started in Gene Orthology and Functional Analysis , 2010, PLoS Comput. Biol..
[65] Peter Uetz,et al. Analysis of protein-protein interactions using array-based yeast two-hybrid screens. , 2009, Methods in molecular biology.
[66] Haian Fu,et al. Protein–Protein Interactions , 1952 .
[67] R. Rapley,et al. Molecular Biomethods Handbook , 1998, Humana Press.
[68] Wei Wang,et al. Identification of Novel Protein-Protein Interactions Using A Versatile Mammalian Tandem Affinity Purification Expression System* , 2003, Molecular & Cellular Proteomics.
[69] Ioannis Xenarios,et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..
[70] Gary D Bader,et al. Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.
[71] G. Cagney,et al. A Skeleton of the Human Protein Interactome , 2005, Cell.
[72] P. Kersey,et al. In Silico Characterization of Proteins: UniProt, InterPro and Integr8 , 2008, Molecular biotechnology.
[73] Gabriel Waksman,et al. Proteomics and protein-protein interactions : biology, chemistry, bionformatics, and drug design , 2005 .
[74] S. Mohammed,et al. Phosphopeptide fragmentation and analysis by mass spectrometry. , 2009, Journal of mass spectrometry : JMS.
[75] Jianhua Ruan,et al. Building and analyzing protein interactome networks by cross-species comparisons , 2010, BMC Systems Biology.
[76] J. Greenblatt,et al. Examining protein protein interactions using endogenously tagged yeast arrays: the cross-and-capture system. , 2007, Genome research.
[77] Beatriz García-Jiménez,et al. Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach , 2010, PloS one.
[78] A. Archakov,et al. Proteomics of mouse liver microsomes: Performance of different protein separation workflows for LC‐MS/MS , 2009, Proteomics.
[79] K. Broo,et al. Orthogonal protein purification--expanding the repertoire of GST fusion systems. , 2008, Protein expression and purification.
[80] Malcolm Buckle,et al. Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip™ based mass spectrometry for the identification of proteins in nucleoprotein interactions , 2007, Nucleic acids research.
[81] R. Ozawa,et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[82] G. Forde. Preparation, analysis and use of an affinity adsorbent for the purification of GST fusion protein. , 2008, Methods in molecular biology.
[83] Priyabrata Pattnaik,et al. Surface plasmon resonance , 2005, Applied biochemistry and biotechnology.
[84] S. Koenig,et al. Surface plasmon resonance/mass spectrometry interface. , 2005, Analytical chemistry.
[85] D Fenyö,et al. Identifying the proteome: software tools. , 2000, Current opinion in biotechnology.
[86] W. Blackstock,et al. Proteome research: Complementarity and limitations with respect to the RNA and DNA worlds , 1997, Electrophoresis.
[87] Y. Hayashizaki,et al. Protein-protein interaction panel using mouse full-length cDNAs. , 2001, Genome research.
[88] Ozlem Keskin,et al. PRISM: protein interactions by structural matching , 2005, Nucleic Acids Res..
[89] K. Büssow,et al. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography , 2003, BMC biotechnology.
[90] S. L. Wong,et al. Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.
[91] B. Taillon,et al. BIA/MS of epitope-tagged peptides directly from E. coli lysate: multiplex detection and protein identification at low-femtomole to subfemtomole levels. , 1999, Analytical chemistry.
[92] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[93] R. Kandpal,et al. The era of 'omics unlimited. , 2009, BioTechniques.
[94] B. Snel,et al. Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.
[95] S. L. Wong,et al. A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.
[96] R. Nussinov,et al. Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[97] Se-Hui Jung,et al. High‐throughput analysis of GST‐fusion protein expression and activity‐dependent protein interactions on GST‐fusion protein arrays with a spectral surface plasmon resonance biosensor , 2006, Proteomics.
[98] Renato Zenobi,et al. Label‐free determination of protein–ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry , 2009, Journal of molecular recognition : JMR.
[99] John A. Robinson,et al. Design of Protein–Protein Interaction Inhibitors Based on Protein Epitope Mimetics , 2009, Chembiochem : a European journal of chemical biology.
[100] Ioannis Xenarios,et al. DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..
[101] K. Garcia,et al. Simplified, Enhanced Protein Purification Using an Inducible, Autoprocessing Enzyme Tag , 2009, PloS one.
[102] H. Hirt,et al. Protein networking: insights into global functional organization of proteomes , 2008, Proteomics.
[103] P. Roepstorff,et al. Combinations of SPR and MS for characterization of native and recombinant proteins in cell lysates , 2006, Molecular biotechnology.
[104] Adam J. Smith,et al. The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..
[105] J. Claverie,et al. What If There Are Only 30,000 Human Genes? , 2001, Science.
[106] A. Valencia,et al. Similarity of phylogenetic trees as indicator of protein-protein interaction. , 2001, Protein engineering.
[107] William Stafford Noble,et al. Kernel methods for predicting protein-protein interactions , 2005, ISMB.
[108] Gabriel Waksman,et al. Proteomics and Protein-Protein Interactions , 2005 .
[109] P. Yaciuk. Co-immunoprecipitation of protein complexes. , 2007, Methods in molecular medicine.
[110] A. Ivanov,et al. Isatin‐binding proteins of rat and mouse brain: Proteomic identification and optical biosensor validation , 2010, Proteomics.
[111] Jean-Philippe Vert,et al. A tree kernel to analyse phylogenetic profiles , 2002, ISMB.
[112] D Nedelkov,et al. Delineation of in vivo assembled multiprotein complexes via biomolecular interaction analysis mass spectrometry , 2001, Proteomics.
[113] R. Nelson,et al. Delineating protein–protein interactions via biomolecular interaction analysis–mass spectrometry , 2003, Journal of molecular recognition : JMR.
[114] Hendrik G. Stunnenberg,et al. Affinity purification of histidine-tagged proteins , 1993, Molecular Biology Reports.
[115] Dong-Soo Han,et al. PreSPI: a domain combination based prediction system for protein-protein interaction. , 2004, Nucleic acids research.
[116] Marc A. Martí-Renom,et al. Prediction of enzyme function by combining sequence similarity and protein interactions , 2008, BMC Bioinformatics.
[117] Haruki Nakamura,et al. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..
[118] Ozlem Keskin,et al. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces , 2005, Bioinform..
[119] J. Yates,et al. Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.
[120] A. Walker-Taylor,et al. Computational Methods for Predicting Protein-Protein Interactions , 2005 .
[121] A. Shevchenko,et al. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.
[122] Martin Vingron,et al. IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..