Relevant bibliographies by topics / Bioinformatics, metalloproteins, metal-binding proteins

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters

Academic literature on the topic 'Bioinformatics, metalloproteins, metal-binding proteins'

Author: Grafiati
Published: 10 March 2023

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Journal articles on the topic "Bioinformatics, metalloproteins, metal-binding proteins"

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Zhang, Yan, and Junge Zheng. "Bioinformatics of Metalloproteins and Metalloproteomes." Molecules 25, no. 15 (2020): 3366. http://dx.doi.org/10.3390/molecules25153366.

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Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, functio
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Andreini, Claudia, and Antonio Rosato. "Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications." International Journal of Molecular Sciences 23, no. 14 (2022): 7684. http://dx.doi.org/10.3390/ijms23147684.

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All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniq
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Wang, Kai, Nan Lyu, Hongjuan Diao, et al. "GM-DockZn: a geometry matching-based docking algorithm for zinc proteins." Bioinformatics 36, no. 13 (2020): 4004–11. http://dx.doi.org/10.1093/bioinformatics/btaa292.

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Abstract Motivation Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing doc
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Monette, Anne, and Andrew J. Mouland. "Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates." Viruses 12, no. 10 (2020): 1179. http://dx.doi.org/10.3390/v12101179.

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Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative dise
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Aramini, James M., and Hans J. Vogel. "Quadrupolar metal ion NMR studies of metalloproteins." Biochemistry and Cell Biology 76, no. 2-3 (1998): 210–22. http://dx.doi.org/10.1139/o98-037.

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We present a summary of the quadrupolar metal ion NMR studies of metalloproteins conducted in our laboratory in recent years. The approaches we employ can be subdivided into two categories: (i) the use of low-frequency metal nuclei to probe metal ion binding sites in small proteins, exemplified by 43Ca NMR studies of alpha-lactalbumins and calcium-binding lysozymes, and (ii) the novel detection of the central transition of half-integer quadrupolar nuclei of moderate frequency bound to large metalloproteins, typified by 27Al, 45Sc, 69,71Ga, and 51V NMR studies of the transferrins. We highlight
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Dudev, Todor, Luis Manuel Frutos, and Obis Castaño. "How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins." Metallomics 12, no. 3 (2020): 363–70. http://dx.doi.org/10.1039/c9mt00283a.

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Arnesano, Fabio, Lucia Banci, and Mario Piccioli. "NMR structures of paramagnetic metalloproteins." Quarterly Reviews of Biophysics 38, no. 2 (2005): 167–219. http://dx.doi.org/10.1017/s0033583506004161.

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1. Introduction 1681.1 Genomic annotation of metalloproteins 1681.2 Why NMR structures? 1681.3 Why paramagnetic metalloproteins? 1692. General theory 1702.1 Nuclear and electron spins 1702.2 Hyperfine coupling 1712.3 The effect of the hyperfine coupling on the NMR shift: the hyperfine shift 1732.4 The effect of the hyperfine coupling on nuclear relaxation 1742.5 Interplay between electron spin properties and features of the NMR spectra 1783. Paramagnetism-based structural restraints 1803.1 Contact shifts and relaxation rates as restraints 1813.2 Locating the metal ion within the protein frame:
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Yu, Yue, Ruobing Wang, and Ruijie D. Teo. "Machine Learning Approaches for Metalloproteins." Molecules 27, no. 4 (2022): 1277. http://dx.doi.org/10.3390/molecules27041277.

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Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein prope
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Carugo, Oliviero. "Metalloproteins: metal binding predicted on the basis of the amino acid sequence." Journal of Applied Crystallography 41, no. 1 (2008): 104–9. http://dx.doi.org/10.1107/s0021889807065235.

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A protein sequence is often insufficient for knowledge of the chemical formula and the properties of the mature molecule that perform its function. Post-translational modifications are very common and most of them cannot be predicted on the basis of the protein sequence alone. A very common chemical modification of proteins that is not directly encoded by a single gene is the complexation with metal cations. Here it is shown that the uptake of metal ions (calcium, cobalt, copper, iron, magnesium, manganese, nickel or zinc) by proteins can be predicted on the basis of the amino acid composition
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Öz, Gülin, Dean L. Pountney, and Ian M. Armitage. "NMR spectroscopic studies of I = 1/2 metal ions in biological systems." Biochemistry and Cell Biology 76, no. 2-3 (1998): 223–34. http://dx.doi.org/10.1139/o98-059.

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This article reviews the use of nuclear magnetic resonance methods of spin 1/2 metal nuclei to probe the metal binding site(s) in a variety of metalloproteins. The majority of the studies have involved native Zn(II) and Ca(II) metalloproteins where there has been isostructural substitution of these metal ions with the I = 1/2 111/113Cd(II) ion. Also included are recent studies that have utilized the 109Ag(I) ion to probe Cu(I) sites in yeast metallothionein and 199Hg(II) as a probe of the metal binding sites in mercury resistance proteins. Pertinent aspects for the optimal execution of these e
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Dissertations / Theses on the topic "Bioinformatics, metalloproteins, metal-binding proteins"

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Roy, Poorna Roy. "Analyzing and classifying bimolecular interactions:I. Effects of metal binding on an iron-sulfur cluster scaffold proteinII. Automatic annotation of RNA-protein interactions for NDB." Bowling Green State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1496412736120654.

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Flowers, Andrew E. "Metal-binding proteins in tropical marine invertebrates." Thesis, Queensland University of Technology, 1995.

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Tsang, Cheuk-nam, and 曾卓南. "Mining of proteins and motifs associated with bismuth binding and monitoring metal uptake in helicobacter pylori by metallomics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46503535.

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Putignano, Valeria. "Bioinformatics tools for metalloprotein analysis." Doctoral thesis, 2019. http://hdl.handle.net/2158/1181143.

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SHARMA, SHAILESH. "Bioinformatics of metal binding proteins and genome wide analysis." Doctoral thesis, 2009. http://hdl.handle.net/2158/485462.

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Sala, Davide. "Application of molecular dynamics to the understanding of metal-binding macromolecules and their adducts." Doctoral thesis, 2019. http://hdl.handle.net/2158/1179863.

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Bilder, Patrick Wallace. "The structural diversity of metal binding sites in bacterial metalloproteins : the disordered iron-binding coil of iron-sulfur cluster protein A and the stable zinc ribbon motif of the carboxyltransferase subunit of acetyl-coa carboxylase." Diss., 2005. http://etd.library.vanderbilt.edu/ETD-db/available/etd-01222006-213113/.

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"Metal contamination and studies of copper-binding proteins from tilapia collected from Shing Mun River." 2005. http://library.cuhk.edu.hk/record=b5896403.

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Szeto Tsz Kwan Leo.<br>Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.<br>Includes bibliographical references (leaves 112-120).<br>Abstracts in English and Chinese.<br>Abstract --- p.i<br>摘要 --- p.iii<br>Acknowledgements --- p.v<br>Table of Contents --- p.vi<br>List of Tables --- p.ix<br>List of Figures --- p.x<br>Abbreviations --- p.xii<br>Chapter Chapter 1 --- Introduction --- p.1<br>Chapter 1.1 --- Heavy metals contaminations in Shing Mun River --- p.1<br>Chapter 1.1 --- Importance of copper regulation and role of liverin copper metabolism --- p.6<br>Chapter 1.1.1 --- Rol
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Books on the topic "Bioinformatics, metalloproteins, metal-binding proteins"

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Kägi, Jeremias H. R., 1930- and Kojima Yutaka 1933-, eds. Metallothionein II: Proceedings of the Second International Meeting on Metallothionein and Other Low Molecular Weight Metal-binding Proteins : Zürich, August 21-24, 1985. Birkhäuser Verlag, 1987.

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Book chapters on the topic "Bioinformatics, metalloproteins, metal-binding proteins"

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"Metal-Binding Proteins." In Encyclopedia of Metalloproteins. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-1533-6_100768.

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Gralka, Ewa, Daniela Valensin, Maurizio Remelli, and Henryk Kozlowski. "Modelling of the Metal Binding Sites in Proteins Involved in Neurodegeneration." In Brain Diseases and Metalloproteins. Pan Stanford Publishing, 2012. http://dx.doi.org/10.1201/b12777-4.

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