Results for 'proteins'

1000+ found
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  1. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of (...)
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  2. ANN Model for Predicting Protein Localization Sites in Cells.Mohammed Nafez Abu Samra, Bilal Ezz El-Din Abed, Hossam Abdel Nasser Zaqout & Samy S. Abu-Naser - 2020 - International Journal of Academic and Applied Research (IJAAR) 4 (9):43-50.
    To automate examination of massive amounts of sequence data for biological function, it is important to computerize interpretation based on empirical knowledge of sequence-function relationships. For this purpose, we have been constructing an Artificial Neural Network (ANN) by organizing various experimental and computational observations as a collection ANN models. Here we propose an ANN model which utilizes the Dataset for UCI Machine Learning Repository, for predicting localization sites of proteins. We collected data for 336 proteins with known localization (...)
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  3.  16
    LRRC8 Proteins Share a Common Ancestor with Pannexins, and May Form Hexameric Channels Involved in Cell‐Cell Communication.Federico Abascal & Rafael Zardoya - 2012 - Bioessays 34 (7):551-560.
  4.  25
    Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube.Hans-Jörg Rheinberger - 1997 - Stanford University Press.
    In this powerful work of conceptual and analytical originality, the author argues for the primacy of the material arrangements of the laboratory in the dynamics of modern molecular biology. In a post-Kuhnian move away from the hegemony of theory, he develops a new epistemology of experimentation in which research is treated as a process for producing epistemic things. A central concern of the book is the basic question of how novelty is generated in the empirical sciences. In addressing this question, (...)
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  5. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
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  6. Framework for a Protein Ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (...)
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  7. Protein Analysis Meets Visual Word Recognition: A Case for String Kernels in the Brain.Thomas Hannagan & Jonathan Grainger - 2012 - Cognitive Science 36 (4):575-606.
    It has been recently argued that some machine learning techniques known as Kernel methods could be relevant for capturing cognitive and neural mechanisms (Jäkel, Schölkopf, & Wichmann, 2009). We point out that ‘‘String kernels,’’ initially designed for protein function prediction and spam detection, are virtually identical to one contending proposal for how the brain encodes orthographic information during reading. We suggest some reasons for this connection and we derive new ideas for visual word recognition that are successfully put to the (...)
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  8. Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  9. Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology.Joseph S. Fruton - 2001 - Journal of the History of Biology 34 (2):413-415.
     
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  10.  11
    The Protein‐Coding Human Genome: Annotating High‐Hanging Fruits.Klas Hatje, Stefanie Mühlhausen, Dominic Simm & Martin Kollmar - 2019 - Bioessays 41 (11):1900066.
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  11. The Representation of Protein Complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and (...)
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  12.  31
    Protein Transport Into Peroxisomes: Knowns and Unknowns.Tânia Francisco, Tony A. Rodrigues, Ana F. Dias, Aurora Barros-Barbosa, Diana Bicho & Jorge E. Azevedo - 2017 - Bioessays 39 (10):1700047.
    Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and rapidly transported into the organelle by a complex machinery. The data gathered in recent years suggest that this machinery operates through a syringe-like mechanism, in which the shuttling receptor PEX5 − the “plunger” − pushes a newly synthesized protein all the way through a peroxisomal transmembrane protein complex − the “barrel” − into the matrix of the organelle. Notably, insertion of cargo-loaded receptor into the “barrel” is an ATP-independent process, whereas (...)
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  13. Where Do You Get Your Protein? Or: Biochemical Realization.Tuomas E. Tahko - 2020 - British Journal for the Philosophy of Science 71 (3):799-825.
    Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for (...)
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  14.  24
    Protein Partners of KCTD Proteins Provide Insights About Their Functional Roles in Cell Differentiation and Vertebrate Development.Mikhail Skoblov, Andrey Marakhonov, Ekaterina Marakasova, Anna Guskova, Vikas Chandhoke, Aybike Birerdinc & Ancha Baranova - 2013 - Bioessays 35 (7):586-596.
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  15.  3
    Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52.Theo Rein - 2020 - Bioessays 42 (7):1900250.
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  16.  14
    Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing.Arnaud Gautier & Alison G. Tebo - 2018 - Bioessays 40 (10):1800118.
    Fluorescence imaging has become an indispensable tool in cell and molecular biology. GFP‐like fluorescent proteins have revolutionized fluorescence microscopy, giving experimenters exquisite control over the localization and specificity of tagged constructs. However, these systems present certain drawbacks and as such, alternative systems based on a fluorogenic interaction between a chromophore and a protein have been developed. While these systems are initially designed as fluorescent labels, they also present new opportunities for the development of novel labeling and detection strategies. This (...)
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  17.  65
    Structure, Function, and Protein Taxonomy.William Goodwin - 2011 - Biology and Philosophy 26 (4):533-545.
    This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing (...)
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  18.  48
    G Protein‐Coupled Receptors Engage the Mammalian Hippo Pathway Through F‐Actin.Laura Regué, Fan Mou & Joseph Avruch - 2013 - Bioessays 35 (5):430-435.
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  19. TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO (...)
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  20.  41
    Proteins, the Chaperone Function and Heredity.Valeria Mosini - 2013 - Biology and Philosophy 28 (1):53-74.
    In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family (...)
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  21.  12
    The Protein Side of the Central Dogma: Permanence and Change.Michel Morange - 2006 - History and Philosophy of the Life Sciences 28 (4):513 - 524.
    There are two facets to the central dogma proposed by Francis Crick in 1957. One concerns the relation between the sequence of nucleotides and the sequence of amino acids, the second is devoted to the relation between the sequence of amino acids and the native three-dimensional structure of proteins. 'Folding is simply a function of the order of the amino acids,' i.e. no information is required for the proper folding of a protein other than the information contained in its (...)
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  22. Proteins and Genes, Singletons and Species.Branko Kozulić - unknown
    Recent experimental data from proteomics and genomics are interpreted here in ways that challenge the predominant viewpoint in biology according to which the four evolutionary processes, including mutation, recombination, natural selection and genetic drift, are sufficient to explain the origination of species. The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. These unique genes and (...), singletons, define the very character of every species. Moreover, the distribution of protein families from the sequenced genomes indicates that the complexity of genomes grows in a manner different from that of self-organizing networks: the dominance of singletons leads to the conclusion that in living organisms a most unlikely phenomenon can be the most common one. In order to provide proper rationale for these conclusions related to the singletons, the paper first treats the frequency of functional proteins among random sequences, followed by a discussion on the protein structure space, and it ends by questioning the idea that protein domains represent conserved units of evolution. (shrink)
     
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  23.  32
    Fluorescent Proteins for Fret Microscopy: Monitoring Protein Interactions in Living Cells.Richard N. Day & Michael W. Davidson - 2012 - Bioessays 34 (5):341-350.
  24.  12
    Protein‐Protein Interactions: Making Sense of Networks Via Graph‐Theoretic Modeling.Nataša Pržulj - 2011 - Bioessays 33 (2):115-123.
  25.  17
    Rnd Proteins: Multifunctional Regulators of the Cytoskeleton and Cell Cycle Progression.Philippe Riou, Priam Villalonga & Anne J. Ridley - 2010 - Bioessays 32 (11):986-992.
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  26.  65
    The Relationship Between Non‐Protein‐Coding DNA and Eukaryotic Complexity.Ryan J. Taft, Michael Pheasant & John S. Mattick - 2007 - Bioessays 29 (3):288-299.
    There are two intriguing paradoxes in molecular biology-the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes-referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases (...)
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  27.  7
    Glycosaminoglycan-Protein Interactions: Definition of Consensus Sites in Glycosaminoglycan Binding Proteins.Ronald E. Hileman, Jonathan R. Fromm, John M. Weiler & Robert J. Linhardt - 1998 - Bioessays 20 (2):156-167.
    Although interactions of proteins with glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are of great biological importance, structural requirements for protein‐GAG binding have not been well‐characterised. Ionic interactions are important in promoting protein‐GAG binding. Polyelectrolyte theory suggests that much of the free energy of binding comes from entropically favourable release of cations from GAG chains. Despite their identical charges, arginine residues bind more tightly to GAGs than lysine residues. The spacing of these residues may determine protein‐GAG affinity and (...)
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  28.  3
    Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces Cerevisiae.Uri Weill, Nir Cohen, Amir Fadel, Shifra Ben‐Dor & Maya Schuldiner - 2019 - Bioessays 41 (8):1800252.
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  29.  13
    Motor Protein Control of Ion Flux is an Early Step in Embryonic Left-Right Asymmetry.Michael Levin - 2003 - Bioessays 25 (10):1002-1010.
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  30.  20
    G Protein‐Coupled Receptors: The Inside Story.Kees Jalink & Wouter H. Moolenaar - 2010 - Bioessays 32 (1):13-16.
  31.  14
    Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC.Jie Zhao, Xiujuan Lei & Fang-Xiang Wu - 2017 - Complexity:1-11.
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  32.  14
    Ribosomal Proteins Control Tumor Suppressor Pathways in Response to Nucleolar Stress.Frédéric Lessard, Léa Brakier-Gingras & Gerardo Ferbeyre - 2019 - Bioessays 41 (3):1800183.
  33.  27
    Protein Folding and Evolution Are Driven by the Maxwell Demon Activity of Proteins.Alejandro Balbín & Eugenio Andrade - 2004 - Acta Biotheoretica 52 (3):173-200.
    In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence of protein folding (...)
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  34.  12
    Quinary Protein Structure and the Consequences of Crowding in Living Cells: Leaving the Test‐Tube Behind.Anna Jean Wirth & Martin Gruebele - 2013 - Bioessays 35 (11):984-993.
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  35. Ribosomal Protein uS3 in Cell Biology and Human Disease: Latest Insights and Prospects.Dmitri Graifer & Galina Karpova - 2020 - Bioessays 42 (12):2000124.
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  36. Computational Protein Design as an Optimization Problem.David Allouche, Isabelle André, Sophie Barbe, Jessica Davies, Simon de Givry, George Katsirelos, Barry O'Sullivan, Steve Prestwich, Thomas Schiex & Seydou Traoré - 2014 - Artificial Intelligence 212:59-79.
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  37.  4
    Protein Kinase Cascades Activated by Stress and Inflammatory Cytokines.John M. Kyriakis & Joseph Avruch - 1996 - Bioessays 18 (7):567-577.
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  38.  41
    SNARE Proteins as Molecular Masters of Interneuronal Communication.Danko D. Georgiev & James F. Glazebrook - 2010 - Biomedical Reviews 21:17-23.
    In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...)
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  39.  34
    Do Protein Motifs Read the Histone Code?Xavier de la Cruz, Sergio Lois, Sara Sánchez-Molina & Marian A. Martínez-Balbás - 2005 - Bioessays 27 (2):164-175.
  40. Investigating Protein-Protein Interfaces in Bacterial Transcription Complexes: A Fragmentation Approach.Patricia C. Burrows - 2003 - Bioessays 25 (12):1150-1153.
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  41.  11
    Protein Dynamics: Complex by Itself.Luigi Leonardo Palese - 2013 - Complexity 18 (3):48-56.
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  42.  10
    Protein Kinase C Binding Partners.Susan Jaken & Peter J. Parker - 2000 - Bioessays 22 (3):245-254.
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  43. Model for DNA and Protein Interactions and the Function of the Operator.Alfred Gierer - 1966 - Nature 212:1480-1481.
    The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .
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  44.  30
    AraC Protein: A Love-Hate Relationship.Robert Schleif - 2003 - Bioessays 25 (3):274-282.
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  45.  21
    Protein Fluctuations Explored by Inelastic Neutron Scattering and Dielectric Relaxation Spectroscopy.G. Chen, P. W. Fenimore, H. Frauenfelder, F. Mezei, J. Swenson & R. D. Young - 2008 - Philosophical Magazine 88 (33-35):3877-3883.
  46. NIPSNAP Protein Family Emerges as a Sensor of Mitochondrial Health.Esmat Fathi, Jay M. Yarbro & Ramin Homayouni - 2021 - Bioessays 43 (6):2100014.
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  47.  34
    Genes, Proteins and Domain-Specificity.G. Marcus - 1999 - Trends in Cognitive Sciences 3 (10):367.
  48.  6
    Putting Proteins in Context.David S. Goodsell - 2012 - Bioessays 34 (9):718-720.
  49. Protein Electron Transfer.Derek S. Bendall & P. M. Wood - 1997 - Bioessays 19 (2):184-184.
     
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  50. Protein Engineering; Principles and Practice, Edited By: JL Cleland and CS Craik.C. MacKellar - 1997 - Human Reproduction and Genetic Ethics 3 (1):17-17.
     
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