Relevant bibliographies by topics / Ligand binding

Academic literature on the topic 'Ligand binding'

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Published: 4 June 2021
Last updated: 7 September 2023

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Journal articles on the topic "Ligand binding"

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Seo, Sangmin, Jonghwan Choi, Soon Kil Ahn, Kil Won Kim, Jaekwang Kim, Jaehyuck Choi, Jinho Kim, and Jaegyoon Ahn. "Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms." Computational and Mathematical Methods in Medicine 2018 (2018): 1–5. http://dx.doi.org/10.1155/2018/6565241.

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We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs) and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or similarity of receptors or ligands. The experimental results show that these new features can be effective in predicting GPCR-ligand binding (average area under the curve [AUC] of 0.944), because they are thought to include hidden properties of good ligand-receptor binding. Using the proposed method, we were able to identify novel ligand-GPCR bindings, some of which are supported by several studies.
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Aziz, Fitri Kusvila, Cantika Nukitasari, Fauziyah Ardli Oktavianingrum, Lita Windy Aryati, and Broto Santoso. "Hasil In Silico Senyawa Z12501572, Z00321025, SCB5631028 dan SCB13970547 dibandingkan Turunan Zerumbon terhadap Human Liver Glycogen Phosphorylase (1l5Q) sebagai Antidiabetes." Jurnal Kimia VALENSI 2, no. 2 (November 30, 2016): 120–24. http://dx.doi.org/10.15408/jkv.v2i2.4170.

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Abstrak Human Liver Glycogen Phosphorylase (HLGP), suatu katalis glikogen yang mengontrol pelepasan glukosa-1-fosfat glikogen dari hati. Enzim ini mempunyai peran sentral dalam luaran glukosa hati sehingga menjadi target obat antidiabetik. Kajian docking dilakukan pada komputer dengan prosesor Intel Pentium, RAM 1 GB dan Windows 7. Ligan yang digunakan adalah senyawa obat (Z12501572, Z00321025, SCB5631028 dan SCB13970547), dataset pembanding aktif glycogen phosphorylase outer dimer site (PYGL-out) dan decoysdari www.dekois.com dan turunan zerumbon. Protein dipisahkan dari ligan nativ dan semua ligan beserta protein dikonversi menggunakan PyRx. Visualisasi interaksi ligan-protein dihasilkan dengan program Protein-Ligand Interaction Profiler (PLIP) dan PyMOL. Senyawa ZER11 memiliki binding energy terbaik, yaitu -7.11 kkal/mol (untuk metode LGA dan GA) dan -4.08 kkal/mol untuk metode SA. Nilai binding energy tersebut lebih rendah dari pada nilai untuk ligan native dan satu dari keempat senyawa obat, terlebih jika dibandingkan dengan bindingaffinity dari dataset dan decoys. Interaksi ligan-protein pada ketiga metode tersebut ditemukan sangat bervariasi. Hal berbeda terjadi untuk metode Vina, bindingenergy ZER11 (-9.9 kkal/mol) lebih baik dibandingkan dengan ligan native dan keempat senyawa obat. Senyawa ZER11 memiliki residu interaksi yang sama dengan ligan native pada TRP67 dan LYS191 untuk metode Vina. Kata kunci: PDBID-1L5Q, AutoDock, docking molekuler, vina, antidiabetes Abstract Human Liver Glycogen Phosphorylase (HLGP) can catalyze glycogen and control the release of glucose-1-phosphate of glycogen from the liver. This enzyme has a central role in output rule of liver glucose as it can be used as an antidiabetic drug targets. Docking studies were carried out on PC with Intel Pentium, 1 GB RAM, in environment of Windows 7. Ligands used are drug compounds (Z12501572, Z00321025, SCB5631028 and SCB13970547), the active dataset comparator wasglycogenphosphorylase outer dimer site (PYGL-out) and decoys from www.dekois.com andzerumbonederivates. Protein was separated from its native ligand and all ligands including the protein were converted to pdbqt using PyRx. The interaction of protein-ligand was visualized using software of PLIP and PyMOL. Compound of ZER11 had the best binding energy were -7.11 kcal/mol (LGA and GA) and -4.08 kcal/mol (SA). The binding energy value was lower than the ligand native and one of the four drug compounds, especially compared with the binding affinity of dataset and decoys. Vice versa, for Vina method, the value of ligand binding protein for ZER11 (-9.9 kcal/mol) was better than the ligand native and all of the fourth drugcompounds. Vina result showed that ZER11 had the same residual interaction as the ligand native, which are TRP67 and LYS191. Keyword: PDBID-1L5Q, AutoDock, molecular docking, vina, antidiabetic DOI: http://dx.doi.org/10.15408/jkv.v0i0.4170
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Williams, Mobolaji. "Derangement model of ligand-receptor binding." Computational and Mathematical Biophysics 10, no. 1 (January 1, 2022): 123–66. http://dx.doi.org/10.1515/cmb-2022-0137.

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Abstract We introduce a derangement model of ligand-receptor binding that allows us to quantitatively frame the question “How can ligands seek out and bind to their optimal receptor sites in a sea of other competing ligands and suboptimal receptor sites?” To answer the question, we first derive a formula to count the number of partial generalized derangements in a list, thus extending the derangement result of Gillis and Even. We then compute the general partition function for the ligand-receptor system and derive the equilibrium expressions for the average number of bound ligands and the average number of optimally bound ligands. A visual model of squares assembling onto a grid allows us to easily identify fully optimal bound states. Equilibrium simulations of the system reveal its extremes to be one of two types, qualitatively distinguished by whether optimal ligand-receptor binding is the dominant form of binding at all temperatures and quantitatively distinguished by the relative values of two critical temperatures. One of those system types (termed “search-limited,” as it was in previous work) does not exhibit kinetic traps and we thus infer that biomolecular systems where optimal ligand-receptor binding is functionally important are likely to be search-limited.
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McNeely, Patrick M., Andrea N. Naranjo, Kimberly Forsten-Williams, and Anne Skaja Robinson. "A2AR Binding Kinetics in the Ligand Depletion Regime." SLAS DISCOVERY: Advancing the Science of Drug Discovery 22, no. 2 (September 27, 2016): 166–75. http://dx.doi.org/10.1177/1087057116667256.

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Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A2A receptor (A2AR) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.
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Micovic, Vuk, Milovan Ivanovic, and Ljiljana Dosen-Micovic. "Structural requirements for ligands of the δ-opioid receptor." Journal of the Serbian Chemical Society 74, no. 11 (2009): 1207–17. http://dx.doi.org/10.2298/jsc0911207m.

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The ?-opioid receptor is sensitive to ligand geometry. In order to assist the synthesis of new ?-selective opioid ligands, the structure elements of ?-selective opioid ligands necessary for their effective binding were investigated. The automated docking procedure with a flexible ligand was used to simulate the binding of 17 ?-selective ligands to the ?-receptor. It was found that voluminous N-alkyl groups reduce the binding potency of naltrindole derivatives by preventing the ligands from adopting the preferred conformation in the receptor. This was confirmed by enantiospecific binding of chiral compounds where only one enantiomer adopts the naltrindole-like preferred conformation in the binding pocket. Voluminous groups replacing the hydroxyl group in the 3-hydroxybenzyl fragment of naltrindole analogs reduce the binding potency due to unfavorable steric interactions with the receptor. The two diastereoisomers of the potent ?-opioid ligand SNC80 confirmed the preferred binding conformation and the major receptor-ligand interactions.
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Tozer, Eileen Collins, Paul E. Hughes, and Joseph C. Loftus. "Ligand binding and affinity modulation of integrins." Biochemistry and Cell Biology 74, no. 6 (December 1, 1996): 785–98. http://dx.doi.org/10.1139/o96-085.

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Integrins are cell adhesion receptors that mediate cell–cell and cell–extracellular matrix interactions. The extracellular domains of these receptors possess binding sites for a diverse range of protein ligands. Ligand binding is divalent cation dependent and involves well-defined motifs in the ligand. Integrins can dynamically regulate their affinity for ligands (inside-out signaling). This ability to rapidly modulate their affinity state is key to their involvement in such processes as cell migration and platelet aggregation. This review will focus on two aspects of integrin function: first, on the molecular basis of ligand–integrin interactions and, second, on the underlying mechanisms controlling the affinity state of integrins for their ligands.Key words: integrins, ligand binding, affinity modulation.
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Marsh, Lorraine. "Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites." BioMed Research International 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/746980.

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Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorableΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorableΔGbecause of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total bindingΔGarising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where “nonspecific” interactions contribute to biological function.
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Weatherman, Ross V., Robert J. Fletterick, and Thomas S. Scanlan. "Nuclear-Receptor Ligands and Ligand-Binding Domains." Annual Review of Biochemistry 68, no. 1 (June 1999): 559–81. http://dx.doi.org/10.1146/annurev.biochem.68.1.559.

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Christensen, U., and L. Mølgaard. "Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change." Biochemical Journal 285, no. 2 (July 15, 1992): 419–25. http://dx.doi.org/10.1042/bj2850419.

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The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.
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Cao, Chen, Lincong Wang, Xiaoyang Chen, Shuxue Zou, Guishen Wang, and Shutan Xu. "Amino Acids in Nine Ligand-Prefer Ramachandran Regions." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/757495.

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Several secondary structures, such asπ-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-preferϕ/ψbox residues are exposed more to solvents, whereas amino acids following ligand-preferϕ/ψbox residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.
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Dissertations / Theses on the topic "Ligand binding"

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Mikolajek, Halina. "Ligand binding to pentraxins." Thesis, University of Southampton, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486591.

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The human pentraxin proteins, serum amyloid P component (SAP) and C-reactive protein (CRP) have emerged as potentially important targets in the treatment of amyloidosis and cardiovascular diseases respectively, although their normal physiological functions are unclear. Structurally highly conserved homologous proteins are present in common experimental animals such as the rat, mouse, rabbit and hamster but there are major differences from the human p,entraxins in their normal behaviour as acute phase proteins, fine ligand specificity and capacity to activate the complement system. . SAP binds to amyloid fibrils ofall types and may contribute to their formation, stabilisation and persistence. In order to extend our current knowledge ofligand recognition by SAP, the crystal structures ofSAP complexed to two ligands, Methylmalonic acid and Phosphatidylethanolamine, have been solved to 1.6 Aand 1.4Aresolution respectively. Since important biological functions ofproteins are often conserved among species, the structural differences between the rat and human pentraxins were investigated. The crystal structure ofrat SAP was solved to 2.2 Aresolution by molecular replacement. This pentameric structure displayed subtle differences in the electrostatic properties. It remains to be determined whether this has an effect on avid binding of SAP to DNA, a functional property ofh~manSAP still poorly understood. CRP, a pentraxin traditionally defined by its binding affinity for PC, was studied in complex with PE. The crystal structure ofthe CRP-PE complex at 2.7 Aresolution revealed that the nitrogen end ofPE dips further downwards into the hydrophobic pocket ofCRP than PC. CRP-mediated complement activation can exacerbate ischemic tissue injury in the heart as well as in the brain. Therefore, knowledge ofthe exact stoichiometry and the protein-protein interactions between CRP and C1q may aid the development ofsmall molecules capable ofdisrupting such protein-protein interactions. Purification of C1q has been achieved by ion-exchange chromatography and gel filtration from BPL paste. Crystallisation trials have been performed, however no crystals have been observed that contain the protein-protein complex.
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Kolstoe, Simon Erik. "Ligand binding to pentraxins." Thesis, University of Southampton, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.416900.

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Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.

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Accurate prediction of binding free energies of protein-ligand system has long been a focus area for theoretical and computational studies; with important implications in fields like pharmaceuticals, enzyme-redesign, etc. The aim of this project was to develop such a predictive model for calculating binding free energies of protein-ligand systems based on the LIE-SASA methods. Many models have been successfully fit to experimental data, but a general predictive model, not reliant on experimental values, would make LIE-SASA a more powerful and widely applicable method. The model was developed such that There is no significant increase in computational time No increase in complexity of system setup No increase in the number of empirical parameters. The method was tested on a small number of protein-ligand systems, selected with certain constraints. This was our training set, from which we obtain the complete expression for binding free energy. Expectedly, there was good agreement with experimental values for the training set On applying our model to a similar sized validation set, with the same selection constraints as for the training set, we achieved even better agreement with experimental results, with lower standard errors. Finally, the model was tested by applying it to a set of systems without such selection constraints, and again found good agreement with experimental values. In terms of accuracy, the model was comparable to a system specific empirical fit that was performed on this set. These encouraging results could be an indicator of generality.
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Whittingham, Jean Lesley. "Ligand binding in hexameric insulins." Thesis, University of York, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385408.

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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 atoms. This function has been formulated in order to reproduce experimental observations of hydrogen-bond geometries. The reorientation of hydrogen atoms and lone-pair orbitals on the formation of hydrogen-bonds is calculated analytically. The experimentally observed water structures of crystals of four biological molecules have been used as model systems for testing the GRID method. It has been shown that the location of well-ordered waters can be predicted accurately. The ability of the GRID method to assist in the assignment of water sites during crystallographic refinement has been demonstrated. It has also been shown that waters in the active site of an enzyme may be both stabilized and displaced by a bound substrate. Ligands have been designed to block the highly conserved host cell receptor site of the influenza virus haemagglutinin in order to prevent the attachment of the virus to the host cells. The protein was mapped energetically by program GRID and specific ligand binding sites were identified. Ligands, which exploited these binding sites, were then designed using computer graphics and energy minimization techniques. Some of the designed ligands were peptides and these were synthesised and assayed. Preliminary results indicate that they may possess anti-influenza activity.
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Kandala, Srikanth. "Diphosphine Ligand Substitution in H4Ru4(CO)12: X-ray Diffraction Structures and Reactivity Studies of the Diphosphine Substituted Cluster Products." Thesis, University of North Texas, 2006. https://digital.library.unt.edu/ark:/67531/metadc5410/.

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The tetraruthenium cluster H4Ru4(CO)12 has been studied for its reactivity with the unsaturated diphosphine ligands (Z)-Ph2PCH=CHPPh2, 4,5-bis (diphenylphosphino)-4-cyclopenten-1,3-dione, bis(diphenyphosphino)benzene and 1,8- bis(diphenyl phosphino)naphthalene under thermal, near-UV photolysis, and Me3NO-assisted activation. All three cluster activation methods promote loss of CO and furnish the anticipated substitution products that possess a chelating diphosphine ligand. Clusters 1, 2, 3 and 4 have been characterized in solution by IR and NMR spectroscopies, and these data are discussed with respect to the crystallographically determined structures for all new cluster compounds. The 31P NMR spectral data and the solid-state structures confirm the presence of a chelating diphosphine ligand in all four new clusters. Sealed NMR tubes containing clusters 1, 2, 3 and 4 were found to be exceeding stable towards near-UV light and temperatures up to ca. 100°C. The surprisingly robust behavior of the new clusters is contrasted with the related cluster Ru3(CO)10(bpcd) that undergoes fragmentation to the donor-acceptor compound Ru2(CO)6(bpcd) and the phosphido-bridged compound Ru2(CO)6 (µ-PPh2)[µ-C=C(PPh2)C(O)CH2C(O)] under mild conditions. The electrochemical properties have been investigated in the case of clusters 1 and 2 by cyclic voltammetry, and the findings are discussed with respect to the reported electrochemical data on the parent cluster H4Ru4(CO)12.
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Chobotova, Katya. "Ligand binding determinants of LIF receptor." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244596.

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Parker, Matthew W. "Molecular Mechanisms of Neuropilin-Ligand Binding." UKnowledge, 2014. http://uknowledge.uky.edu/biochem_etds/15.

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Neuropilin (Nrp) is an essential cell surface receptor with dual functionality in the cardiovascular and nervous systems. The first identified Nrp-ligand family was the Semaphorin-3 (Sema3) family of axon repulsion molecules. Subsequently, Nrp was found to serve as a receptor for the vascular endothelial growth factor (VEGF) family of pro-angiogenic cytokines. In addition to its physiological role, VEGF signaling via Nrp directly contributes to cancer stemness, growth, and metastasis. Thus, the Nrp/VEGF signaling axis is a promising anti-cancer therapeutic target. Interestingly, it has recently been shown that Sema3 and VEGF are functionally opposed to one another, with Sema3 possessing potent endogenous anti-angiogenic activity and VEGF serving as an attractive cue for neuronal axons. We hypothesized that direct competition for an overlapping binding site within the Nrp extracellular domain may explain the observed functional competition between VEGF and Sema3. To test this hypothesis we have separately investigated the mechanisms of VEGF and Sema3 binding to Nrp. Utilizing structural biology coupled with biophysics and biochemistry we have identified both distinct and common mechanisms that facilitate the interaction between Nrp and these two ligand families. Specifically, we have identified an Nrp binding pocket to which these ligands competitively bind. The Sema3 family uniquely requires proteolytic activation in order to engage this overlapping binding site. These findings provide critical mechanistic insight into VEGF and Sema3 mediated physiology. Additionally, these data have informed the development of small molecules, peptides, and soluble receptor fragments that function as potent and selective inhibitors of VEGF/Nrp binding with exciting therapeutic potential for treating cancer.
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Sleigh, Sara. "Ligand binding by an oligopeptide receptor." Thesis, University of York, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242157.

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Nandigrami, Prithviraj. "Cooperative allosteric ligand binding in calmodulin." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977.

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Books on the topic "Ligand binding"

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Bellelli, Andrea, and Jannette Carey. Reversible Ligand Binding. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781119238508.

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Khan, Masood N., and John W. A. Findlay, eds. Ligand-Binding Assays. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2009. http://dx.doi.org/10.1002/9780470541517.

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H, Sawyer William, ed. Quantitative characterization of ligand binding. New York: Wiley-Liss, 1995.

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Stoddard, Barry L., ed. Computational Design of Ligand Binding Proteins. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3569-7.

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Protein-ligand interactions: Methods and applications. 2nd ed. New York: Humana Press, 2013.

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Krishna, Mallia A., and Smith Paul K, eds. Immobilized affinity ligand techniques. San Diego: Academic Press, 1992.

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Podjarny, Alberto, Annick P. Dejaegere, and Bruno Kieffer, eds. Biophysical Approaches Determining Ligand Binding to Biomolecular Targets. Cambridge: Royal Society of Chemistry, 2011. http://dx.doi.org/10.1039/9781849732666.

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E, Harding S., and Chowdhry Babur Z, eds. Protein-ligand interactions, structure and spectroscopy: A practical approach. Oxford: Oxford University Press, 2001.

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

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Ligand-receptor energetics: A guide for the perplexed. New York: Wiley, 1997.

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Book chapters on the topic "Ligand binding"

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Fischer, Gabriele, Annemarie Unger, W. Wolfgang Fleischhacker, Cécile Viollet, Jacques Epelbaum, Daniel Hoyer, Ina Weiner, et al. "Ligand Binding." In Encyclopedia of Psychopharmacology, 709. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_3350.

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Fischer, Gabriele, Annemarie Unger, W. Wolfgang Fleischhacker, Cécile Viollet, Jacques Epelbaum, Daniel Hoyer, Ina Weiner, et al. "Labeled Ligand Binding." In Encyclopedia of Psychopharmacology, 685. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_3342.

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Bonomo, R. P., D. Grasso, G. Grasso, V. Guantieri, G. Impellizzeri, C. Rosa, D. Milardi, G. Pappalardo, G. Tabbì, and E. Rizzarelli. "Metal Binding to Prion Protein." In Metal-Ligand Interactions, 21–39. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-010-0191-5_2.

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Lambert, Bernard, and Jean-Bernard Le Pecq. "Pharmacology of DNA Binding Drugs." In DNA—Ligand Interactions, 141–57. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_9.

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Tuckwell, Danny S., and Martin J. Humphries. "Ligand Binding Sites Within the Integrins." In Integrin-Ligand Interaction, 199–217. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_9.

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Holdgate, Geoffrey A., and Paul E. Hemsley. "Ligand Discovery: High-Throughput Binding: Fluorescence ()." In Protein-Ligand Interactions, 231–46. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_10.

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Kauffman, Chris, and George Karypis. "Ligand-Binding Residue Prediction." In Introduction to Protein Structure Prediction, 343–68. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2010. http://dx.doi.org/10.1002/9780470882207.ch16.

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Burgot, Jean-Louis. "Ligand Binding to Macromolecules." In Thermodynamics in Bioenergetics, 139–47. Boca Raton, FL : CRC Press, 2019. | “A science publishers book.”: CRC Press, 2019. http://dx.doi.org/10.1201/9781351034227-23.

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Sharp, Kim A. "Statistical Thermodynamics of Binding and Molecular Recognition Models." In Protein-Ligand Interactions, 1–22. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch1.

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Tangemann, Kirsten, and Jürgen Engel. "Binding Studies of Integrins with Their Respective Ligands." In Integrin-Ligand Interaction, 85–100. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_3.

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Conference papers on the topic "Ligand binding"

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Dzichenka, Yaraslau, Michail Shapira, Sergei Usanov, Marina Savić, Ljubica Grbović, Jovana Ajduković, and Suzana Jovanović-Šanta. "NOVEL LIGANDS OF HUMAN CYP7 ENZYMES – POSSIBLE MODULATORS OF CHOLESTEROL BLOOD LEVEL: COMPUTER SIMULATION STUDIES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.435d.

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Our in vitro studies showed that a couple of perspective steroidal derivatives showed previously biomedical potential via enzyme inhibition, receptor binding or antiproliferative effect against the cancer cells of reproductive tissues are able to bind to human CYP7 enzymes – key enzymes taking part in hydroxylation of cholesterol, 25-, 27-hydroxycholesterol and a number of steroidal hormones. In silico screening of binding affinity of the modified steroids toward CYP7 enzymes showed that interaction energy for the new ligands is comparable with consequent values, calculated for the ‘essential’ substrates of the enzymes – cholestenone (CYP7A1) and DHEA (CYP7B1). However, no correlation between binding energy and the affinity of the ligand was found. Novel ligands interact with conserved amino acids taking part in stabilization of natural substrates of CYP7 enzymes. A couple of structural features, governing ligand binding, were identified. Among which are planar structure of A-ring for CYP7A1 ligands, absence of many polar fragments in side-chain and presence of polar group at C3 position. Analysis of the docking results showed that CYP7B1 higher selectivity in comparison with CYP7A1 is connected by the structure of the cavity formed by α-helices I and B`. The data obtained will be used for the explanation of ligand specificity of human sterol- hydroxylases.
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Chesla, Scott E., and Cheng Zhu. "A Novel Method for Determination of Kinetic Rates of Surface Bound Receptor-Ligand Binding." In ASME 1996 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1996. http://dx.doi.org/10.1115/imece1996-1200.

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Abstract Cellular adhesion is important to many biological processes. These adhesive interactions are mediated by specific binding of cell surface receptors to their ligands. An important determinant of the receptor-ligand interaction is their kinetic rates. Existing bulk chemistry approaches for measuring rate constants require at least one of the reactants to be in solution. Therefore, at least one molecular species is able to move in three dimensions, and there is no force acting on the bond. This kind of rate constants is referred to as 3-D rates in the present paper. In contrast, in the case of cell adhesion, the motions of both molecular species are restricted to two-dimensional because both receptor and ligand are anchored to a surface (and the kinetic rates are thereby referred to as 2-D rates). In addition, dislodging forces usually exist which affect the dissociation. Because of these differences, the (3-D) rate constants measured via traditional approaches cannot be directly applied to the analysis of receptor-ligand binding kinetics in cell adhesion.
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Lim, Manko, Timothy A. Jackson, and Philip A. Anfinrud. "Ultrafast Near-IR Spectroscopy of Carbonmonoxymyoglobin: the Dynamics of Protein Relaxation." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb3.

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The conformation of a protein often influences its activity, yielding a structure-function relationship. X-ray diffraction studies have shown that the tertiary structures of ligated and deligated myoglobin (Mb) are somewhat different1. Consequently, dissociation of a ligand from Mb triggers a transition between the two tertiary conformations. The potential energy gradient causing this change is developed at the heme; the iron prefers to be in the plane of the porphyrin in ligated Mb but is displaced 0.5 Å from the plane of the porphyrin in deoxy Mb. The dynamics of this conformational transition may influence the dynamics of rebinding ligands, implying that protein dynamics are also functionally important. For example, the dynamics of ligand recombination with Mb following photolysis of MbCO or MbO2 in low-temperature glasses are similar2. In contrast, Mb expurgates CO with far greater efficiency than O2 when photolysis is carried out at biologically important temperatures3. Since protein motion is inhibited at low temperatures, protein relaxation likely accounts for the temperature-dependent difference in the quantum yield of photodissociation. The ability to discriminate against the binding and storage of CO is functionally important as endogenously produced CO would otherwise compete effectively with O2 for binding sites. A steric mechanism for discriminating against the binding of CO, involving the distal histidine, is well known. The dynamics of protein relaxation evidently provide a mechanism for discriminating against the storage of CO. We have investigated the dynamics of protein relaxation in order to probe this mechanism and thereby elucidate the relation between protein dynamics and function.
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Christensen, Ulla. "Kinetics of piasminogen-activation. Effects of ligands binding to the AH-site of plasminogen." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644420.

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Detailed kinetic studies of the urokinase catalysed conversion of Lys-77- and Val-440-plasminogens in the presence and absence of ligands binding to the AH-site of the plasminogens shows that the effects of such ligand-binding correspond with a model of the activation reaction in which the effective Km and kc decreases, but kc/Km increases when the ligands bind. Apparently plasminogen with a free AH-site is a less specific substrate for urokinase, than is plasminogen with an AH-site-bound ligand.The AH-site is a weak lysine binding site of plasminogen located in the mini plasminogen part (Val-440-Asn-790) of plasminogen and is suggested to participate in the binding of the plasminogens to undegraded fibrin.
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Hsu, Kai-Cheng, Yen-Fu Chen, and Jinn-Moon Yang. "Binding Affinity Analysis of Protein-Ligand Complexes." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.46.

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Chen, Ruobing, Katya Scheinberg, and Brian Y. Chen. "Aligning ligand binding cavities by optimizing superposed volume." In 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2012. http://dx.doi.org/10.1109/bibm.2012.6392629.

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Kauffman, Chris, Huzefa Rangwala, and George Karypis. "IMPROVING HOMOLOGY MODELS FOR PROTEIN-LIGAND BINDING SITES." In Proceedings of the CSB 2008 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2008. http://dx.doi.org/10.1142/9781848162648_0019.

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Lee, Ling Wei, and Andrzej Bargiela. "Prediction And Modelling Of Ligand-Binding Sites Using." In 26th Conference on Modelling and Simulation. ECMS, 2012. http://dx.doi.org/10.7148/2012-0096-0102.

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Yeh, Hsin-Yi (Cindy), Shawna Thomas, and Nancy M. Amato. "Using motion planning to rank ligand binding affinity." In the 6th ACM Conference. New York, New York, USA: ACM Press, 2015. http://dx.doi.org/10.1145/2808719.2811445.

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Wall, Michael E. "Ligand Binding, Protein Fluctuations, And Allosteric Free Energy." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345620.

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Reports on the topic "Ligand binding"

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Chung, Arthur. Development of Novel Ligand Binding Assay for Estrogen Receptor. Fort Belvoir, VA: Defense Technical Information Center, April 2000. http://dx.doi.org/10.21236/ada390487.

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Chung, Arthur C. Development of a Novel Ligand Binding Assay for Estrogen Receptor. Fort Belvoir, VA: Defense Technical Information Center, April 2002. http://dx.doi.org/10.21236/ada421346.

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Arnold, John. Potential New Ligand Systems for Binding Uranyl Ions in Seawater Environments. Office of Scientific and Technical Information (OSTI), December 2014. http://dx.doi.org/10.2172/1166963.

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Trewhella, J. The role of low frequency collective modes in biological function: Ligand binding and cooperativity in calcium-binding proteins. Office of Scientific and Technical Information (OSTI), November 2000. http://dx.doi.org/10.2172/768788.

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Arnold, John. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study. Office of Scientific and Technical Information (OSTI), January 2015. http://dx.doi.org/10.2172/1183657.

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Arnold, John. Selectivity in Ligand Binding to Uranyl Compounds: A Synthetic, Structural, Thermodynamic and Computational Study. Office of Scientific and Technical Information (OSTI), December 2017. http://dx.doi.org/10.2172/1414423.

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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Wuttke, Deborah S. Breast Cancer Therapeutics, Environmental Estrogens, and the Estrogens Receptor (ER); Characterization of the Diverse Ligand Binding Properties of the ER. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada398995.

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Wuttke, Deborah S. Breast Cancer Therapeutics, Environmental Estrogens, and the Estrogen Receptor (ER); Characterization of the Diverse Ligand Binding Properties of the ER. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada408777.

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Wuttke, Deborah S. Breast Cancer Therapeutics, Environmental Estrogens, and the Estrogen Receptor (ER); Characterization of the Diverse Ligand Binding Properties of the ER. Fort Belvoir, VA: Defense Technical Information Center, July 2003. http://dx.doi.org/10.21236/ada420485.

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