Relevant bibliographies by topics / Macromolecular ligand

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Academic literature on the topic 'Macromolecular ligand'

Author: Grafiati
Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "Macromolecular ligand"

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Saravanan, S. E., R. Karthi, K. Sathish, K. Kokila, R. Sabarinathan, and K. Sekar. "MLDB: macromolecule ligand database." Journal of Applied Crystallography 43, no. 1 (2009): 200–202. http://dx.doi.org/10.1107/s0021889809048626.

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MLDB (macromolecule ligand database) is a knowledgebase containing ligands co-crystallized with the three-dimensional structures available in the Protein Data Bank. The proposed knowledgebase serves as an open resource for the analysis and visualization of all ligands and their interactions with macromolecular structures. MLDB can be used to search ligands, and their interactions can be visualized both in text and graphical formats. MLDB will be updated at regular intervals (weekly) with automated Perl scripts. The knowledgebase is intended to serve the scientific community working in the area
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Smart, Oliver S., Vladimír Horský, Swanand Gore, et al. "Validation of ligands in macromolecular structures determined by X-ray crystallography." Acta Crystallographica Section D Structural Biology 74, no. 3 (2018): 228–36. http://dx.doi.org/10.1107/s2059798318002541.

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Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or rep
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Clowney, Les, John D. Westbrook, and Helen M. Berman. "CIF Applications. XI.A La Mode: a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models." Journal of Applied Crystallography 32, no. 1 (1999): 125–33. http://dx.doi.org/10.1107/s0021889898005160.

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The macromolecular Crystallographic Information File (mmCIF) dictionary [Fitzgeraldet al.(1997).The Macromolecular Crystallographic Information File Dictionary, http://ndbserver.rutgers.edu/mmcif] provides a comprehensive description of chemical components used as models in the crystallographic refinement of macromolecular structures. A new ligand and monomer object data environment namedA La Modeis described for building chemical-component models in the mmCIF representation from surveys of high-resolution small-molecule crystal structures. Examples of the application of this system are presen
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Eidelman, O., P. Yani, H. C. Englert, H. G. Lang, R. Greger, and Z. I. Cabantchik. "Macromolecular conjugates of transport inhibitors: new tools for probing topography of anion transport proteins." American Journal of Physiology-Cell Physiology 260, no. 5 (1991): C1094—C1103. http://dx.doi.org/10.1152/ajpcell.1991.260.5.c1094.

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Macromolecular-conjugated, water-soluble, membrane-impermeant compounds were designed and assessed as topological probes for chloride-transporting agencies. The novel compounds were derivatives of either disulfonic stilbene (DS) and benzylaminoethylsulfonate (BS), "classical" inhibitors of erythrocyte chloride-bicarbonate exchange, or of phenylanthranilates (PA), high-affinity blockers of epithelial chloride channels. Covalent reactive derivatives of various DS, BS, and PA were synthesized and coupled either directly to polyethylene glycol or via spacer arms of different lengths to dextrans. T
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Carolan, C. G., and V. S. Lamzin. "Automated identification of crystallographic ligands using sparse-density representations." Acta Crystallographica Section D Biological Crystallography 70, no. 7 (2014): 1844–53. http://dx.doi.org/10.1107/s1399004714008578.

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A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the met
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Borbulevych, Oleg Y., Joshua A. Plumley, Roger I. Martin, Kenneth M. Merz, and Lance M. Westerhoff. "Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics programDivConinto thePHENIXrefinement package." Acta Crystallographica Section D Biological Crystallography 70, no. 5 (2014): 1233–47. http://dx.doi.org/10.1107/s1399004714002260.

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Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requiresa prioriunderstanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-sca
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Nicholls, Robert A. "Ligand fitting withCCP4." Acta Crystallographica Section D Structural Biology 73, no. 2 (2017): 158–70. http://dx.doi.org/10.1107/s2059798316020143.

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Crystal structures of protein–ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein–ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. TheCCP4 suite contains a number of software tools that facilitate this task:AceDRGfor the creation of ligand descrip
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Golden, Emily A., and Alice Vrielink. "Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function." Australian Journal of Chemistry 67, no. 12 (2014): 1751. http://dx.doi.org/10.1071/ch14337.

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Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study
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Zheng, Heping, Mahendra Chordia, David Cooper, et al. "Check your metal - not every density blob is a water molecule." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1483. http://dx.doi.org/10.1107/s2053273314085167.

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Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemist
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Beshnova, Daria A., Joana Pereira, and Victor S. Lamzin. "Estimation of the protein–ligand interaction energy for model building and validation." Acta Crystallographica Section D Structural Biology 73, no. 3 (2017): 195–202. http://dx.doi.org/10.1107/s2059798317003400.

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Macromolecular X-ray crystallography is one of the main experimental techniques to visualize protein–ligand interactions. The high complexity of the ligand universe, however, has delayed the development of efficient methods for the automated identification, fitting and validation of ligands in their electron-density clusters. The identification and fitting are primarily based on the density itself and do not take into account the protein environment, which is a step that is only taken during the validation of the proposed binding mode. Here, a new approach, based on the estimation of the major
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Dissertations / Theses on the topic "Macromolecular ligand"

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Shell, Elizabeth. "Chemical Unfolding and Macromolecular Crowding of Alpha-1-Acid Glycoprotein." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1115047649.

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Khalid, Syma. "Molecular simulation studies of the interaction between DNA and a novel macromolecular ligand." Thesis, University of Warwick, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406780.

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Mukherjee, Prasenjit. "Use of molecular modeling tools in the elucidation of ligand-macromolecular interactions and applications in structure-based drug design /." Full text available from ProQuest UM Digital Dissertations, 2008. http://0-proquest.umi.com.umiss.lib.olemiss.edu/pqdweb?index=0&did=1850501401&SrchMode=1&sid=4&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1277323802&clientId=22256.

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Thesis (Ph.D.)--University of Mississippi, 2008.<br>Typescript. Vita. Major professor: Mitchell A. Avery Includes bibliographical references (leaves 246-259). Also available online via ProQuest to authorized users.
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Wade, R. C. "Ligand-macromolecule interactions." Thesis, University of Oxford, 1988. http://ora.ox.ac.uk/objects/uuid:576ce119-6a93-4eb0-a7e4-1f2513736dbd.

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The optimisation of ligand-macromolecule interactions is fundamental to the design of therapeutic agents. The GRID method is a procedure for determining energetically favourable ligand binding sites on molecules of known structure using an empirical energy potential. In this thesis, it has been extended, tested, and then applied to the design of anti-influenza agents. In the GRID method, the energy of a hydrogen-bond is determined by a function which is dependent on the length of the hydrogen-bond, its orientation at the hydrogen-bond donor and acceptor atoms, and the chemical nature of these
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Preston, Sarah Suzanne. "Metal coordination directed folding of intramolecularly hydrogen-bonded dendrons." The Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=osu1135869971.

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Recht, Raphaël. "Mise au point de méthodes de détection d’interaction ligand-macromolécule par RMN du 19F." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAJ055/document.

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Les interactions biologiques sont régies par des mécanismes complexes, qui mêlent différentes échelles, de temps comme de taille. C’est le cas du ribosome, un complexe nucléoprotéique responsable de la traduction de l’ARNm en protéines, et ce faisant, une cible thérapeutique primordiale. Or la taille du ribosome procaryote 70S (2.4 MDa) rend difficile l’applications des techniques classiques de criblage de ligands. Au cours de ma thèse, j’ai exploré la possibilité d’utiliser la RMN du fluor pour caractériser les interactions entre des ligands et le ribosome procaryote. Cette approche a été mot
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Ohyama, Tsuyoshi. "Thermodynamic studies of ligand binding to biological macromolecules by isothermal titration calorimetry /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu148794844082652.

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Amerein, Béatrice. "Modelisation et representation dynamique de macromolecules biologiques." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13040.

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Van, Kralingen Leon. "Ligand modification of Pluronic F108 for use in immobilized metal affinity separation of bio-macromolecules." Thesis, Stellenbosch : Stellenbosch University, 2002. http://hdl.handle.net/10019.1/52918.

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Thesis (MSc)--Stellenbosch University, 2002.<br>ENGLISH ABSTRACT: Inthis work we aim to put into place a system to separate or immobilise biomacromolecules by means ofimmobilised transition metal ions like nickel(II) or copper(II). Although the concept of immobilised metal affmity chromatography (IMAC) has been around since the early 1960's, the metal ions were always immobilised by covalent modification of the support matrix. Recently the concept of IMAC was applied to membranes, and again the metal ion was immobilised by covalent modification of the membrane surface. Inthis study we c
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Yee, Sidney. "Solution-State Proton Nuclear Magnetic Resonance (NMR) Spectroscopic Studies of the Active Site of Myoglobins in Various Ligated States: Models for Macromolecule-Substrate Binding and Advancement of Paramagnetic NMR Techniques." PDXScholar, 1993. https://pdxscholar.library.pdx.edu/open_access_etds/1253.

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This work focuses on pigmy sperm whale and horse myoglobins (Mbs), which are distinguished by a single heme pocket residue variant in the CD3 position, when the heme iron is in the +3 oxidation state (i.e. the met form). The strategy employed is as follows: (i) assign heme peripheral protons; (ii) assign the amino acid residues from the heme cavity; (iii) assess the dynamics of ligand binding in the active site by means of hydrogen Iability, solvent isotope effects, and heme-insertion isomer trapping, all by NMR methods. The results of these studies portray dynamic solution structure of the Mb
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Books on the topic "Macromolecular ligand"

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Roque, Ana Cecília A., ed. Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-244-5.

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Woodbury, Charles P. Introduction to macromolecular binding equilibria. CRC Press, 2008.

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Ligand-macromolecular interactions in drug discovery: Methods and protocols. Springer, 2009.

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Biochemical Pharmacology Symposium (4th 1989 New Haven, Conn.). NMR methods for elucidating macromolecule-ligand interactions: An approach to drug design : proceedings of the Fourth Biochemical Pharmacology Symposium, New Haven, CT, 27-29 July 1989. Edited by Handschumacher Robert E, Armitage Ian M, and Welch Arnold D. Pergamon Press, 1990.

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Thermodynamic theory of site-specific binding processes in biological macromolecules. Cambridge University Press, 1995.

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Wyman, Jeffries. Binding and linkage: Functional chemistry of biological macromolecules. University Science Books, 1990.

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Conley, Edward C. The ion channel factsbook. Academic Press, 1996.

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Conley, Edward C. The ion channel factsbook. Academic Press, Harcourt Brace & Co., 1996.

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J, Brammar W., ed. The ion channel factsbook. Academic Press, Harcourt Brace & Co., 1996.

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Introduction to Macromolecular Binding Equilibria. CRC, 2007.

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Book chapters on the topic "Macromolecular ligand"

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Alagona, Giuliano, Caterina Ghio, and Peter A. Kollman. "Computational Approaches to the Study of Protein — Ligand Interactions." In Macromolecular Biorecognition. Humana Press, 1987. http://dx.doi.org/10.1007/978-1-4612-4600-8_2.

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Viegas, Aldino, Anjos L. Macedo, and Eurico J. Cabrita. "Ligand-Based Nuclear Magnetic Resonance Screening Techniques." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_6.

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Quaglia, Milena, and Ersilia De Lorenzi. "Capillary Electrophoresis in Drug Discovery." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_12.

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Pramanik, Aladdin. "Ligand–Macromolecule Interactions in Live Cells by Fluorescence Correlation Spectroscopy." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_18.

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Pina, Ana Sofia, Abid Hussain, and Ana Cecília A. Roque. "An Historical Overview of Drug Discovery." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_1.

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Horiuchi, Kurumi Y., and Haiching Ma. "Fluorescence Polarization and Time-Resolved Fluorescence Resonance Energy Transfer Techniques for PI3K Assays." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_10.

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Meng, Lihao, Dawn Mattoon, and Paul Predki. "Small Molecule Protein Interaction Profiling with Functional Protein Microarrays." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_11.

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Minunni, Maria, and Anna Rita Bilia. "SPR in Drug Discovery: Searching Bioactive Compounds in Plant Extracts." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_13.

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Slon-Usakiewicz, Jacek J., and Peter Redden. "Application of Frontal Affinity Chromatography with Mass Spectrometry (FAC–MS) for Stereospecific Ligand–Macromolecule Interaction, Detection and Screening." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_14.

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Siegel, Marshall M. "GPC Spin Column HPLC–ESI-MS Methods for Screening Drugs Noncovalently Bound to Proteins." In Ligand-Macromolecular Interactions in Drug Discovery. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_15.

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Conference papers on the topic "Macromolecular ligand"

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Russo, M. V., A. Furlani, G. lucci, and G. Polzonetti. "Poly(n,n-dimethylpropargylamine): a /spl pi/-conjugated polymer as macromolecular ligand." In International Conference on Science and Technology of Synthetic Metals. IEEE, 1994. http://dx.doi.org/10.1109/stsm.1994.835412.

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Masso, Majid. "Knowledge-based scoring function derived from atomic tessellation of macromolecular structures for prediction of protein-ligand binding affinity." In 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2012. http://dx.doi.org/10.1109/bibmw.2012.6470315.

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Velazquez-Campoy, Adrian. "Unspecific Cooperative Ligand Binding to One-Dimensional Lattice-like Macromolecules." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345633.

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"Analysis of ligand binding to macromolecules using kinetic and polynomial approaches." In 22nd International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand (MSSANZ), Inc., 2017. http://dx.doi.org/10.36334/modsim.2017.c6.jamal.

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Reports on the topic "Macromolecular ligand"

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Yee, Sidney. Solution-State Proton Nuclear Magnetic Resonance (NMR) Spectroscopic Studies of the Active Site of Myoglobins in Various Ligated States: Models for Macromolecule-Substrate Binding and Advancement of Paramagnetic NMR Techniques. Portland State University Library, 2000. http://dx.doi.org/10.15760/etd.1252.

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