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  • 1
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    Detecting protein function and protein-protein interactions from genome sequences (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-31
    Description: A computational method is proposed for inferring protein interactions from genome sequences on the basis of the observation that some pairs of interacting proteins have homologs in another organism fused into a single protein chain. Searching sequences from many genomes revealed 6809 such putative protein-protein interactions in Escherichia coli and 45,502 in yeast. Many members of these pairs were confirmed as functionally related; computational filtering further enriches for interactions. Some proteins have links to several other proteins; these coupled links appear to represent functional interactions such as complexes or pathways. Experimentally confirmed interacting pairs are documented in a Database of Interacting Proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marcotte, E M -- Pellegrini, M -- Ng, H L -- Rice, D W -- Yeates, T O -- Eisenberg, D -- P01 GM 31299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 30;285(5428):751-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA-Department of Energy Laboratory of Structural Biology and Molecular Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10427000" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism/physiology ; Binding Sites ; *Computational Biology ; Databases, Factual ; Escherichia coli/genetics ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; *Genome ; Genome, Bacterial ; Genome, Fungal ; Humans ; Models, Biological ; Proteins/chemistry/genetics/metabolism/*physiology ; *Sequence Homology, Amino Acid ; *Sequence Homology, Nucleic Acid ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Biochemistry. Proteins in a small world (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeates, Todd O -- Beeby, Morgan -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1882-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA90024-1569, USA. yeates@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185587" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolic Networks and Pathways ; Mutation ; Protein Binding ; *Protein Interaction Mapping ; Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Use of logic relationships to decipher protein network organization (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: A major focus of genome research is to decipher the networks of molecular interactions that underlie cellular function. We describe a computational approach for identifying detailed relationships between proteins on the basis of genomic data. Logic analysis of phylogenetic profiles identifies triplets of proteins whose presence or absence obey certain logic relationships. For example, protein C may be present in a genome only if proteins A and B are both present. The method reveals many previously unidentified higher order relationships. These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowers, Peter M -- Cokus, Shawn J -- Eisenberg, David -- Yeates, Todd O -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2246-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618515" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Physiological Phenomena ; Bacterial Proteins/*analysis/chemistry/*physiology ; *Computational Biology ; *Genome ; *Genome, Bacterial ; Logic ; Movement ; Phylogeny ; Protein Array Analysis ; *Protein Interaction Mapping ; Proteins/*analysis/genetics/*physiology ; Shikimic Acid/metabolism ; Virulence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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