Search results for 'protein folding problem' (try it on Scholar)

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  1. Xiaolong Zhang & Wen Cheng (2008). An Improved Tabu Search Algorithm for 3D Protein Folding Problem. In. In Tu-Bao Ho & Zhi-Hua Zhou (eds.), Pricai 2008: Trends in Artificial Intelligence. Springer. 1104--1109.score: 270.0
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  2. Jeffry L. Ramsey (2007). Calibrating and Constructing Models of Protein Folding. Synthese 155 (3):307 - 320.score: 152.0
    Prediction is more than testing established theory by examining whether the prediction matches the data. To show this, I examine the practices of a community of scientists, known as threaders, who are attempting to predict the final, folded structure of a protein from its primary structure, i.e., its amino acid sequence. These scientists employ a careful and deliberate methodology of prediction. A key feature of the methodology is calibration. They calibrate in order to construct better models. The construction leads (...)
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  3. Alan Levin (2010). A Top-Down Approach to a Complex Natural System: Protein Folding. [REVIEW] Axiomathes 20 (4):423-437.score: 146.0
    We develop a general method for applying functional models to natural systems and cite recent progress in protein modeling that demonstrates the power of this approach. Functional modeling constrains the range of acceptable structural models of a system, reduces the difficulty of finding them, and improves their fidelity. However, functional models are distinctly different from the structural models that are more commonly applied in science. In particular, structural and functional models ask different questions and provide different kinds of answers. (...)
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  4. Michel Morange (2006). The Protein Side of the Central Dogma: Permanence and Change. History and Philosophy of the Life Sciences 28 (4):513 - 524.score: 114.0
    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 (...)
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  5. Alejandro Balbín & Eugenio Andrade (2004). Protein Folding and Evolution Are Driven by the Maxwell Demon Activity of Proteins. Acta Biotheoretica 52 (3).score: 112.0
    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 (...)
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  6. H. H. Pattee (2013). Epistemic, Evolutionary, and Physical Conditions for Biological Information. Biosemiotics 6 (1):9-31.score: 105.0
    The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation is (...)
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  7. Robert L. Baldwin (1994). Finding Intermediates in Protein Folding. Bioessays 16 (3):207-210.score: 84.0
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  8. M. Januar, A. Sulaiman & L. T. Handoko (2010). Conformation Changes and Protein Folding Induced by Φ4 Interaction. In. In Harald Fritzsch & K. K. Phua (eds.), Proceedings of the Conference in Honour of Murray Gell-Mann's 80th Birthday. World Scientific. 472.score: 84.0
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  9. Vishwanath R. Lingappa, D. Thomas Rutkowski, Ramanujan S. Hegde & Olaf S. Andersen (2002). Conformational Control Through Translocational Regulation: A New View of Secretory and Membrane Protein Folding. Bioessays 24 (8):741-748.score: 84.0
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  10. Jörg Martin & F.‐Ulrich Hartl (1994). Molecular Chaperones in Cellular Protein Folding. Bioessays 16 (9):689-692.score: 84.0
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  11. C. Robert Matthews & Mark R. Hurle (1987). Mutant Sequences as Probes of Protein Folding Mechanisms. Bioessays 6 (6):254-257.score: 84.0
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  12. МОЛЕКУЛЯРНА БІОФІЗИКА (2004). Clustering Monte Carlo Simulations of the Hierarchical Protein Folding on a Simple Lattice Model. Complexity 7 (9):22-23.score: 84.0
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  13. Thomas E. Creighton (1992). What the Papers Say: Protein Folding Pathways Determined Using Disulphide Bonds. Bioessays 14 (3):195-199.score: 84.0
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  14. Peter Lund (1994). The Chaperonin Cycle and Protein Folding. Bioessays 16 (4):229-231.score: 84.0
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  15. Gabriela Ochoa, Gabi Escuela & Natalio Krasnogor (2006). Artificial Life and Bioinformatics-Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. In O. Stock & M. Schaerf (eds.), Lecture Notes in Computer Science. Springer-Verlag. 3871--247.score: 84.0
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  16. Massimo Pigliucci (2010). Genotype–Phenotype Mapping and the End of the ‘Genes as Blueprint’ Metaphor. Philosophical Transactions Royal Society B 365:557–566.score: 81.0
    In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...)
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  17. Valeria Mosini (2013). Proteins, the Chaperone Function and Heredity. Biology and Philosophy 28 (1):53-74.score: 74.0
    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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  18. Gustavo Caetano‐Anollés & Jay Mittenthal (2010). Exploring the Interplay of Stability and Function in Protein Evolution. Bioessays 32 (8):655-658.score: 74.0
  19. Anna Jean Wirth & Martin Gruebele (2013). Quinary Protein Structure and the Consequences of Crowding in Living Cells: Leaving the Test‐Tube Behind. Bioessays 35 (11):984-993.score: 74.0
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  20. C. K. Raju (2004). The Electrodynamic 2-Body Problem and the Origin of Quantum Mechanics. Foundations of Physics 34 (6):937-962.score: 72.0
    We numerically solve the functional differential equations (FDEs) of 2-particle electrodynamics, using the full electrodynamic force obtained from the retarded Lienard–Wiechert potentials and the Lorentz force law. In contrast, the usual formulation uses only the Coulomb force (scalar potential), reducing the electrodynamic 2-body problem to a system of ordinary differential equations (ODEs). The ODE formulation is mathematically suspect since FDEs and ODEs are known to be incompatible; however, the Coulomb approximation to the full electrodynamic force has been believed to (...)
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  21. Patrick W. K. Lee & Gustavo Leone (1994). Reovirus Protein ?1: From Cell Attachment to Protein Oligomerization and Folding Mechanisms. Bioessays 16 (3):199-206.score: 72.0
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  22. Hong‐Fang Ji, Lei Chen, Ying‐Ying Jiang & Hong‐Yu Zhang (2009). Evolutionary Formation of New Protein Folds is Linked to Metallic Cofactor Recruitment. Bioessays 31 (9):975-980.score: 56.7
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  23. Minglei Wang, Simina Maria Boca, Rakhee Kalelkar, Jay E. Mittenthal & Gustavo Caetano-Anollés (2006). A Phylogenomic Reconstruction of the Protein World Based on a Genomic Census of Protein Fold Architecture. Complexity 12 (1):27-40.score: 56.7
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  24. Shu Quan & James Ca Bardwell (2012). Chaperone Discovery. Bioessays 34 (11):973-981.score: 56.0
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  25. Franco Giorgi, Luis Emilio Bruni & Roberto Maggio (2013). Semiotic Selection of Mutated or Misfolded Receptor Proteins. Biosemiotics 6 (2):177-190.score: 46.0
    Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed by these receptors is assumed to be causally predetermined by the cell genome. However, this mechanism does not fully explain how differentiated cells have come to express specific receptor repertoires and which combinatorial codes have been explored to activate their associated signaling pathways. (...)
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  26. Aare Abroi & Julian Gough (2011). Are Viruses a Source of New Protein Folds for Organisms?–Virosphere Structure Space and Evolution. Bioessays 33 (8):626-635.score: 42.0
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  27. John N. Prebble (2013). Contrasting Approaches to a Biological Problem: Paul Boyer, Peter Mitchell and the Mechanism of the ATP Synthase, 1961–1985. [REVIEW] Journal of the History of Biology 46 (4):699-737.score: 42.0
    Attempts to solve the puzzling problem of oxidative phosphorylation led to four very different hypotheses each of which suggested a different view of the ATP synthase, the phosphorylating enzyme. During the 1960s and 1970s evidence began to accumulate which rendered Peter Mitchell’s chemiosmotic hypothesis, the novel part of which was the proton translocating ATP synthase (ATPase), a plausible explanation. The conformational hypothesis of Paul Boyer implied an enzyme where ATP synthesis was driven by the energy of conformational changes in (...)
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  28. Mehmet Ozansoy & Yagmur Denizhan (2009). The Endomembrane System: A Representation of the Extracellular Medium? [REVIEW] Biosemiotics 2 (3):255-267.score: 36.0
    Both prokaryotic and eukaryotic cells share the basic mechanisms of secretory protein synthesis. However, unlike prokaryotes, eukaryotic cells posses a system of compartments, the so-called endomembrane system, which are involved in the synthesis process. A comparison of the prokaryotic and eukaryotic protein synthesis processes and particularly the observation of the functional and structural similarity between the prokaryotic cell membrane (the interface to the cell exterior) and the membrane of the eukaryotic endoplasmic reticulum (one of the compartments within the (...)
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  29. David Morris (1999). The Fold and the Body Schema in Merleau-Ponty and Dynamic Systems Theory. Chiasmi International 1:275-286.score: 30.0
    Contemporary thought, whether it be in psychology, biology, immunology, philosophy of perception or philosophy of mind, is confronted with the breakdown of barriers between organism and environment, self and other, subject and object, perceiver and perceived. In this paper I show how Merleau-Ponty can help us think about this problem, by attending to a methodological theme in the background of his dialectical conception of embodiment. In La structure du comportement, Merleau-Ponty conceives life as extension folding back upon itself (...)
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  30. Jon Williamson (2006). Introduction. Journal of Logic, Language and Information 15 (1-2):1-3.score: 29.0
    The need for a coherent answer to this question has become increasingly urgent in the past few years, particularly in the field of artificial intelligence. There, both logical and probabilistic techniques are routinely applied in an attempt to solve complex problems such as parsing natural language and determining the way proteins fold. The hope is that some combination of logic and probability will produce better solutions. After all, both natural language and protein molecules have some structure that admits logical (...)
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  31. Andreas Hüttemann & Alan C. Love (2011). Aspects of Reductive Explanation in Biological Science: Intrinsicality, Fundamentality, and Temporality. British Journal for the Philosophy of Science 62 (3):519-549.score: 28.0
    The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...)
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  32. Jonathan Birch (2012). Robust Processes and Teleological Language. European Journal for Philosophy of Science 3 (3):299-312.score: 28.0
    I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” (...)
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  33. E. M. (1999). The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965-1991 - Part I: Prelude to Prions. Studies in History and Philosophy of Science Part C 30 (1):1-19.score: 28.0
    Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis (...)
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  34. Alexander Powell (2009). Molecules, Cells and Minds: Aspects of Bioscientific Explanation. Dissertation, University of Exeterscore: 28.0
    In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon looks mechanistic, (...)
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  35. J. P. Liautard (1999). Analytical Background and Discussion of the Chaperone Model of Prion Diseases. Acta Biotheoretica 47 (3-4).score: 28.0
    It is generally accepted that prion infection is due solely to a protein i.e. the protein-only hypothesis. The essential constituent of infectious prions is the scrapie prion protein (PrPSc) which is chemically indistinguishable from the normal, cellular protein (PrPC) but exhibits distinct secondary and tertiary structure. This very unusual feature seems to be in contradiction with a major paradigm of present structural biology stated by Anfinsen: a protein folds to the most stable conformation, this means (...)
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  36. Alvaro Moreno Bergareche & Julio Fernández (1988). EI Código Genético Como Punto Crítico En la Evolución de Los Sistemas Biológicos. Theoria 4 (1):177-196.score: 27.0
    Firstly we consider the new results about enzymatic capabilities in the RNA. In this framework we analyse the sequence-folding duality as a precursor of the genotype/phenotype duality. We discuss then which are the evolutive potentialities and limitations for a system with the absence and the presence of a nucleic acid to proteins translator code. We study the arise of the code in the living systems as a form of deep interlooking between the logic of the machinery and its hardware, (...)
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  37. Alvaro Moreno Bergareche & Julio Fernández (1988). EI código genético como punto crítico en la evolución de los sistemas biológicos. Theoria 4 (1):177-196.score: 27.0
    Firstly we consider the new results about enzymatic capabilities in the RNA. In this framework we analyse the sequence-folding duality as a precursor of the genotype/phenotype duality. We discuss then which are the evolutive potentialities and limitations for a system with the absence and the presence of a nucleic acid to proteins translator code. We study the arise of the code in the living systems as a form of deep interlooking between the logic of the machinery and its hardware, (...)
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  38. David Penny (2005). An Interpretive Review of the Origin of Life Research. Biology and Philosophy 20 (4):633-671.score: 24.0
    Life appears to be a natural property of matter, but the problem of its origin only arose after early scientists refuted continuous spontaneous generation. There is no chance of life arising ‘all at once’, we need the standard scientific incremental explanation with large numbers of small steps, an approach used in both physical and evolutionary sciences. The necessity for considering both theoretical and experimental approaches is emphasized. After describing basic principles that are available (including the Darwin-Eigen cycle), the search (...)
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  39. J. B. Edelmann & M. J. Denton (2007). The Uniqueness of Biological Self-Organization: Challenging the Darwinian Paradigm. Biology and Philosophy 22 (4):579-601.score: 24.0
    Here we discuss the challenge posed by self-organization to the Darwinian conception of evolution. As we point out, natural selection can only be the major creative agency in evolution if all or most of the adaptive complexity manifest in living organisms is built up over many generations by the cumulative selection of naturally occurring small, random mutations or variants, i.e., additive, incremental steps over an extended period of time. Biological self-organization—witnessed classically in the folding of a protein, or (...)
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  40. Michael Bacharach (1992). Backward Induction and Beliefs About Oneself. Synthese 91 (3):247 - 284.score: 24.0
    According to decision theory, the rational initial action in a sequential decision-problem may be found by backward induction or folding back. But the reasoning which underwrites this claim appeals to the agent's beliefs about what she will later believe, about what she will later believe she will still later believe, and so forth. There are limits to the depth of people's beliefs. Do these limits pose a threat to the standard theory of rational sequential choice? It is argued, (...)
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  41. Paul Davies, The Origin of Life II: How Did It Begin?score: 24.0
    The problem of how a mixture of chemicals can spontaneously transform themselves into even a simple living organism remains one of the great outstanding challenges to science. Various primordial soup theories have been proposed in which chemical self- organization brings about the required level of complexity. Major conceptual obstacles remain, however, such as the emergence of the genetic code, and the “chicken-and-egg” problem concerning which came first: nucleic acids or proteins. Currently fashionable is the so-called RNA world theory, (...)
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  42. Ying-Hua Lv Lian-Peng Zhao, Ming-Hai Yao Chun Li & Xi-Zi Jin (2010). An s-Curve-Based Approach of Identifying Biological Sequences. Acta Biotheoretica 58 (1).score: 24.0
    The main idea of S-curve diagram is to assign different angle values (from 0° to 180°) to different nucleotide acid residues or to different protein amino acids, and then according to cos α j and sin α j , the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so (...)
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  43. Hans-Jörg Rheinberger (1993). Experiment and Orientation: Early Systems of in Vitro Protein Synthesis. [REVIEW] Journal of the History of Biology 26 (3):443 - 471.score: 24.0
    The living world is one of complexity, the result of innumerable interactions among organisms, cells, molecules. In analyzing a problem, the biologist is constrained to focus on a fragment of reality, on a piece of the universe which he arbitrarily isolates to define certain of its parameters.In biology, any study thus begins with the choice of a “system.” On this choice depend the experimenter's freedom to maneuver, the nature of the questions he is free to ask, and even, often, (...)
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  44. James Maclaurin (1998). Reinventing Molecular Weismannism: Information in Evolution. [REVIEW] Biology and Philosophy 13 (1):37-59.score: 24.0
    Molecular Weismannism is the claim that: In the development of an individual, DNA causes the production both of DNA (genetic material) and of protein (somatic material). The reverse process never occurs. Protein is never a cause of DNA. This principle underpins both the idea that genes are the objects upon which natural selection operates and the idea that traits can be divided into those that are genetic and those that are not. Recent work in developmental biology and in (...)
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  45. J. Aracena & J. Demongeot (2004). Mathematical Methods for Inferring Regulatory Networks Interactions: Application to Genetic Regulation. Acta Biotheoretica 52 (4).score: 24.0
    This paper deals with the problem of reconstruction of the intergenic interaction graph from the raw data of genetic co-expression coming with new technologies of bio-arrays (DMA-arrays, protein-arrays, etc.). These new imaging devices in general only give information about the asymptotical part (fixed configurations of co-expression or limit cycles of such configurations) of the dynamical evolution of the regulatory networks (genetic and/or proteic) underlying the functioning of living systems. Extracting the casual structure and interaction coefficients of a gene (...)
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  46. Catherine Kendig, Reconstructing the Concept of Homology for Genomics. Pittsburgh/London Colloquium on Philosophy of Biology and Neuroscience, University of London. Online at PhilSci Archive.score: 24.0
    Homology has been one of, if not the most, fecund concepts which has been used towards the understanding of the genomes of the model organisms. The evidence for this claim can be supported best with an examination of current research in comparative genomics. In comparative genomics, the information of genes or segments of the genome, and their location and sequence, are used to search for genes similar to them, known as 'homologues'. Homologues can be either within that same organism (paralogues), (...)
     
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  47. M. N. Feleafel & Z. M. Mirdad (2013). Hazard and Effects of Pollution by Lead on Vegetable Crops. Journal of Agricultural and Environmental Ethics 26 (3):547-567.score: 24.0
    Lead (Pb) contamination of the environment is an important human health problem. Children are vulnerable to Pb toxicity; it causes damage to the central nervous system and, in some extreme cases, can cause death. Lead is widespread, especially in the urban environment, and is present in the atmosphere, soil, water and food. Pb tends to accumulate in surface soil because of its low solubility, mobility, and relative freedom from microbial degradation of this element in the soil. Lead is present (...)
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  48. Arlene D. Albert & Philip L. Yeagle (1995). The Determination of Rhodopsin Structure May Require Alternative Approaches. Behavioral and Brain Sciences 18 (3):469-469.score: 24.0
    The structure of rhodopsin is a subject of intense interest. Solving the structure by traditional methods has proved exceedingly challenging. It may therefore be useful to confront the problem by a combination of alternate techniques. These include FTIR (Fourier transform infrared spectroscopy) and AFM (atomic force microscopy) on the intact protein. Furthermore, additional insights may be gained through structural investigations of discrete rhodopsin domains.
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  49. Patricia M. Clissold & Roy Bicknell (2003). The Thioredoxin-Like Fold: Hidden Domains in Protein Disulfide Isomerases and Other Chaperone Proteins. Bioessays 25 (6):603-611.score: 24.0
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  50. Yair Neuman & Ophir Nave (2008). On the Semio-Mathematical Nature of Codes. Biosemiotics 1 (1):99-111.score: 24.0
    The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” (...)
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