Relevant bibliographies by topics / Protein; Ligands

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Protein; Ligands'

Author: Grafiati
Published: 4 June 2021
Last updated: 16 February 2022

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Journal articles on the topic "Protein; Ligands"

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Karasev, Dmitry, Boris Sobolev, Alexey Lagunin, Dmitry Filimonov, and Vladimir Poroikov. "Prediction of Protein–ligand Interaction Based on Sequence Similarity and Ligand Structural Features." International Journal of Molecular Sciences 21, no. 21 (2020): 8152. http://dx.doi.org/10.3390/ijms21218152.

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Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the or
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Southern, Craig, Jennifer M. Cook, Zaynab Neetoo-Isseljee та ін. "Screening β-Arrestin Recruitment for the Identification of Natural Ligands for Orphan G-Protein–Coupled Receptors". Journal of Biomolecular Screening 18, № 5 (2013): 599–609. http://dx.doi.org/10.1177/1087057113475480.

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A variety of G-protein–coupled receptor (GPCR) screening technologies have successfully partnered a number of GPCRs with their cognate ligands. GPCR-mediated β-arrestin recruitment is now recognized as a distinct intracellular signaling pathway, and ligand-receptor interactions may show a bias toward β-arrestin over classical GPCR signaling pathways. We hypothesized that the failure to identify native ligands for the remaining orphan GPCRs may be a consequence of biased β-arrestin signaling. To investigate this, we assembled 10 500 candidate ligands and screened 82 GPCRs using PathHunter β-arr
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Finkina, Ekaterina I., Daria N. Melnikova, Ivan V. Bogdanov, et al. "Impact of Different Lipid Ligands on the Stability and IgE-Binding Capacity of the Lentil Allergen Len c 3." Biomolecules 10, no. 12 (2020): 1668. http://dx.doi.org/10.3390/biom10121668.

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Previously, we isolated the lentil allergen Len c 3, belonging to the class of lipid transfer proteins, cross-reacting with the major peach allergen Pru p 3 and binding lipid ligands. In this work, the allergenic capacity of Len c 3 and effects of different lipid ligands on the protein stability and IgE-binding capacity were investigated. Impacts of pH and heat treating on ligand binding with Len c 3 were also studied. It was shown that the recombinant Len c 3 (rLen c 3) IgE-binding capacity is sensitive to heating and simulating of gastroduodenal digestion. While being heated or digested, the
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Raingeval, Claire, and Isabelle Krimm. "NMR investigation of protein–ligand interactions for G-protein coupled receptors." Future Medicinal Chemistry 11, no. 14 (2019): 1811–25. http://dx.doi.org/10.4155/fmc-2018-0312.

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In this review, we report NMR studies of ligand–GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a
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Hutchens, T. W., and J. O. Porath. "Protein recognition of immobilized ligands: promotion of selective adsorption." Clinical Chemistry 33, no. 9 (1987): 1502–8. http://dx.doi.org/10.1093/clinchem/33.9.1502.

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Abstract We are using simple immobilized ligands to evaluate the biochemistry and mechanisms of selective, high-affinity, protein adsorption events. Several specific means have recently been developed to more selectively utilize the favorable entropy changes associated with the displacement of protein-bound water during the formation and stabilization of protein-ligand recognition events. For protein and peptide immobilization these include, besides hydrophobic interaction, for example, metal ion, pi-electron-mediated, and thiophilic interactions. This latter type of protein-ligand recognition
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Mary, Sophie, Jean-Alain Fehrentz, Marjorie Damian, et al. "How ligands and signalling proteins affect G-protein-coupled receptors' conformational landscape." Biochemical Society Transactions 41, no. 1 (2013): 144–47. http://dx.doi.org/10.1042/bst20120267.

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The dynamic character of GPCRs (G-protein-coupled receptors) is essential to their function. However, the details of how ligands and signalling proteins stabilize a receptor conformation to trigger the activation of a given signalling pathway remain largely unexplored. Multiple data, including recent results obtained with the purified ghrelin receptor, suggest a model where ligand efficacy and functional selectivity are directly related to different receptor conformations. Importantly, distinct effector proteins (G-proteins and arrestins) as well as ligands are likely to affect the conformatio
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Galano-Frutos, Juan J., M. Carmen Morón, and Javier Sancho. "The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin." Physical Chemistry Chemical Physics 17, no. 43 (2015): 28635–46. http://dx.doi.org/10.1039/c5cp04504e.

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Ferreira de Freitas, Renato, and Matthieu Schapira. "A systematic analysis of atomic protein–ligand interactions in the PDB." MedChemComm 8, no. 10 (2017): 1970–81. http://dx.doi.org/10.1039/c7md00381a.

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We compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins representing 750 873 protein–ligand atomic interactions, and analyzed the frequency, geometry and the impact of each interaction type. The most frequent ligand–protein atom pairs can be clustered into seven interaction types.
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Mehta, Simpi, and Seema R. Pathak. "INSILICO DRUG DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL COUMARIN DERIVATIVES AS ANTI-CANCER AGENTS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (2017): 335. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16826.

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins usi
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GORETZKI, Lothar, and Barbara M. MUELLER. "Low-density-lipoprotein-receptor-related protein (LRP) interacts with a GTP-binding protein." Biochemical Journal 336, no. 2 (1998): 381–86. http://dx.doi.org/10.1042/bj3360381.

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The low-density-lipoprotein-receptor-related protein (LRP) binds and internalizes numerous ligands, including lipoproteins, proteinase–inhibitor complexes and others. We have shown previously that LRP-mediated ligand internalization is dependent on cAMP-dependent protein kinase (PKA) activity. Here, we investigated whether ligation of LRP increases the intracellular cAMP level and PKA activity via a stimulatory GTP-binding protein. Treatment of LRP-expressing cell lines with the LRP ligands lactoferrin or urokinase-type plasminogen activator caused a significant elevation in cAMP and stimulate
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Dissertations / Theses on the topic "Protein; Ligands"

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Almeida, T. B. "Identification and optimisation of ligands to target protein-protein interactions : EB1-SxIP proteins." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3004877/.

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End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule growing ends which has a fundamental role in microtubule polymerisation. EB1 regulates the microtubule dynamic behaviour, through protein recruitment, and has been associated with several disease states, such as cancer and neuronal diseases. Diverse EB1 binding partners are recognised through a conserved SxIP motif within an intrinsically disordered region enriched with basic, serine and proline residues. Crystal structure of EB1 in complex with a peptide containing the SxIP motif
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Hassan, Hani Mutlak Abdullah. "Chemical Synthesis of Protein Ligands." Thesis, University of Manchester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501975.

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Larsson, Emma. "Calcium-dependent affinity ligands for protein purification." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278695.

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The rapid growth of the biopharmaceutical industry has led to increasing demands on the protein production process. An important aspect is the yield of functional protein, which can be greatly affected by the choice of downstream purification. Purification based on acidic elution can be an issue for pH-sensitive proteins, since dramatic changes in pH can lead to protein aggregation and loss of function. The harsh, acidic elution conditions used in conventional purification of antibodies by Protein A affinity chromatography can thus be problematic. To address this, a calcium-dependent protein d
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Street, Ian Philip. "Protein - carbohydrate interactions in glycogen phosphorylase." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/25049.

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It has long been observed that some organo-fluorine compounds exhibit enhanced biological activity over their non-fluorinated precursors, however reasons for these unusual properties still remain poorly understood. An explanation which has been widely used relates to the ability of the C-F fragment of the analog to participate in hydrogen-bonding interactions with its protein receptor. For this reason, fluorinated carbohydrates have been used as hydrogen-bonding probes with a number of proteins. Thus there exists a need for a systematic investigation into the hydrogen-bonding ability of the C
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Linhult, Martin. "Protein engineering to explore and improve affinity ligands." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3632.

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<p>In order to produce predictable and robust systems forprotein purification and detection, well characterized, small,folded domains descending from bacterial receptors have beenused. These bacterial receptors, staphylococcal protein A (SPA)and streptococcal protein G (SPG), possess high affinity to IgGand / or HSA. They are composed of repetitive units in whicheach one binds the ligand independently. The domains foldindependently and are very stable. Since the domains also havewellknown three-dimensional structures and do not containcysteine residues, they are very suitable as frameworks for
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Georgiou, Charis. "Rational design of isoform specific ligands." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28713.

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Cyclophilins (Cyp) are proteins that catalyze the interconversion of trans/cis isomers of proline belonging to the peptidyl-prolyl isomerases family (PPIase). In addition to their PPIase activity, Cyps have diverse biological roles and have been implicated in a number of different diseases such as HIV-1 and HCV. Although several Cyp inhibitors have been reported in the literature, none are able to inhibit with high specificity various Cyp isoforms. To facilitate the development of isoform-specific Cyp ligands, we have pursued detailed studies of Cyp dynamics and ligand binding thermodynamics u
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Duraj-Thatte, Anna. "Fluorescent GFP chromophores as potential ligands for various nuclear receptors." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44764.

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Nuclear receptors are ligand activated transcription factors, where upon binding with small molecule ligands, these proteins are involved in the regulation of gene expression. To date there are approximately 48 human nuclear receptors known, involved in multiple biological and cellular processes, ranging from differentiation to maintenance of homeostasis. Due to their critical role in transcriptional regulation, these receptors are implicated in several diseases. Currently, 13% of prescribed drugs in the market are NR ligands for diseases such as cancer, diabetes and osteoporosis. In addition
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Tosch, Paul. "Investigations of ephrin ligands during development." Title page, abstract and table of contents only, 2002. http://web4.library.adelaide.edu.au/theses/09PH/09pht713.pdf.

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"May 2002." Addendum inside back cover. Bibliography: p. 139-157. Aims to isolate ephrin ligands from Drosophila melanogaster and analyse their involvement in Drosophila deveopment. Also investigates the potential of ephrin B-1 as a causative gene in the human condition Aicardi's syndrome.
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Robinson, Daniel D. "Applications of pattern recognition and pattern analysis to molecule design." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343465.

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Boussert, Stéphanie Van Dorsselaer Alain Giralt Ernest. "Structural studies of proteins and protein complexes by mass spectrometry and atomic force microscopy." Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/977/01/BOUSSERT_Stephanie_2008.pdf.

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Books on the topic "Protein; Ligands"

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Neve, Kim A., ed. Functional Selectivity of G Protein-Coupled Receptor Ligands. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-335-0.

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Roterman, Irena, and Leszek Konieczny, eds. Self-Assembled Molecules – New Kind of Protein Ligands. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-65639-7.

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Siegfried, Schwarz. Molecules of life & mutations: Understanding diseases by understanding proteins. Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Karger, 2002.

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

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Johnson, Michael L., Jo M. Holt, and Gary K. Ackers. Biothermodynamics. Elsevier/Academic Press, 2011.

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Easterfield, Howard James. Analogues of phosphotyrosine: New components of ligands for protein tyrosine kinase enzymes. University of Birmingham, 1999.

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Hernandez, Marta. The study of ligand binding specificities of the lipid binding proteins: Recombinant human a-tocopherol transport protein (a-ttp), supernatant protein factor (spf) and S. cerevisiae Sec 14p for vitamin e (rrr-a-tocopherol) and other hydrophobic ligands. Brock University, Dept. of Biotechnology, 2003.

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Nava, Phillip J. Synthesis of fluorescent analogues of a-tocopherol as ligands for the human a-tocopherol transfer protein (a-TTP). Brock University, Centre for Biotechnology, 2006.

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Book chapters on the topic "Protein; Ligands"

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Wang, Jianpeng. "Protein Ligands Engineering." In Springer Theses. Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-53399-4_3.

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Dobrodziej, Jennifer, Hanqing Dong, Kurt Zimmermann, and Christopher M. Hickey. "Evaluating Ligands for Ubiquitin Ligases Using Affinity Beads." In Targeted Protein Degradation. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1665-9_4.

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Pitt, William R., Mark D. Calmiano, Boris Kroeplien, Richard D. Taylor, James P. Turner, and Michael A. King. "Structure-Based Virtual Screening for Novel Ligands." In Protein-Ligand Interactions. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_19.

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Kay, Brian K., Michael D. Scholle, and Fred J. Stevens. "EH Domains and Their Ligands." In Modular Protein Domains. Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603611.ch14.

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Ciulli, Alessio. "Biophysical Screening for the Discovery of Small-Molecule Ligands." In Protein-Ligand Interactions. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_13.

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Rybarska, Joanna, Barbara Piekarska, Barbara Stopa, Grzegorz Zemanek, Leszek Konieczny, and Irena Roterman. "Supramolecular Systems as Protein Ligands." In Self-Assembled Molecules – New Kind of Protein Ligands. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65639-7_1.

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Christianson, D. W., and W. N. Lipscomb. "Reaction Coordinate Approach to the Binding of Ligands to Carboxypeptidase A." In Protein Structure and Protein Engineering. Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-74173-9_8.

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Sathish, Jean Gerard, and Reginald James Matthews. "SHP-1 twelve years on: structure, ligands, substrates and biological roles." In Protein Phosphatases. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-40035-6_15.

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Sousa, Isabel T., and M. Ângela Taipa. "Biomimetic Affinity Ligands for Protein Purification." In Methods in Molecular Biology. Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-977-2_20.

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Sousa, Isabel T., and M. Ângela Taipa. "Biomimetic Affinity Ligands for Protein Purification." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0775-6_14.

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Conference papers on the topic "Protein; Ligands"

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Timkin, Pavel, E. Timofeev, A. Chupalov, and Evgeniy Borodin. "ANALYSIS AND SELECTION OF LIGANDS FOR TRPM8 USING HARD DOCKING AND MACHINE LEARNING." In XIV International Scientific Conference "System Analysis in Medicine". Far Eastern Scientific Center of Physiology and Pathology of Respiration, 2020. http://dx.doi.org/10.12737/conferencearticle_5fe01d9b233509.17835494.

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In this work, using the in-silico experiment modeling method, the receptor and its ligands were docked in order to obtain the data necessary to study the possibility of using machine learning and hard intermolecular docking methods to predict potential ligands for various receptors. The protein TRPM8 was chosen, which is a member of the TRP superfamily of proteins and its classic agonist menthol as a ligand. It is known that menthol is able to bind to tyrosine 745 of the B chain. To carry out all the manipulations, we used the Autodock software and a special set of graphic tools designed to wo
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Howl, John. "Chimeric ligands for G-protein-coupled receptors." In VIth Conference Biologically Active Peptides. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199903009.

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ERGUNER, BEKIR, MASAHIRO HATTORI, SUSUMU GOTO, and MINORU KANEHISA. "CHARACTERIZING COMMON SUBSTRUCTURES OF LIGANDS FOR GPCR PROTEIN SUBFAMILIES." In Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010). IMPERIAL COLLEGE PRESS, 2010. http://dx.doi.org/10.1142/9781848166585_0003.

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Cuppoletti, John. "Composite Synthetic Membranes Containing Native and Engineered Transport Proteins." In ASME 2008 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2008. http://dx.doi.org/10.1115/smasis2008-449.

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Our membrane transport protein laboratory has worked with material scientists, computational chemists and electrical and mechanical engineers to design bioactuators and sensing devices. The group has demonstrated that it is possible to produce materials composed native and engineered biological transport proteins in a variety of synthetic porous and solid materials. Biological transport proteins found in nature include pumps, which use energy to produce gradients of solutes, ion channels, which dissipate ion gradients, and a variety of carriers which can either transport substances down gradie
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Timmons, Sheila, and Jack Hawiger. "REGULATION OF PLATELET RECEPTORS FOR FIBRINOGEN AND VON WILLEBRAND FACTOR BY PROTEIN KINASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644674.

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Positive and negative regulation of platelet receptors for adhesive proteins, fibrinogen (F) and von Willebrand Factor (vWF) determines whether binding of these ligands will or will not take place. We have shown previously that ADP stimulates and cyclic AMP inhibits binding of F and vWF to human platelets. Now we show that positive regulation of F and vWF binding to platelets via the glycoprotein 11b/1111a complex is dependent on platelet Protein Kinase C, a calcium- and phospholipid-dependent enzyme. A potent activator of Protein Kinase C, phorbol-12-myristoyl-13-acetate (PMA) induced saturab
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Tobysheva, P. D., L. A. Khamidullina, I. S. Puzyrev, and A. V. Pestov. "Biological activity of complexes based on polycarbonyl ligands: assessment of the mode of action using molecular docking." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.249.

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Herre, Jurgen, Hans Gronlund, Heather Brookes, et al. "Allergens As Immuno-Modulatory Proteins: The Cat Dander Protein FelD1 Enhances Toll-Like Receptor Activation By Lipid Ligands." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a1415.

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Zhu, X. D., Y. Y. Fei, J. P. Landry, and Y. S. Sun. "Label-Free Screening Small Molecule Compounds for Protein Ligands with Optically Detected Microarrays." In Bio-Optics: Design and Application. OSA, 2011. http://dx.doi.org/10.1364/boda.2011.bmc7.

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Zhu, X. D., Y. Y. Fei, J. P. Landry, and Y. S. Sun. "Screening Small Molecule Compounds for Protein Ligands with Label-Free, Optically Detected Microarrays." In Biomedical Optics. OSA, 2010. http://dx.doi.org/10.1364/biomed.2010.btud13.

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Lee, Hae-Jeong, Marvi A. Matos, Lisa Pakstis, Marcus T. Cicerone, and Joy P. Dunkers. "Quantitation of Laminin Adsorbed Onto Polydimethylsiloxane Surfaces Using Various Treatment Protocols." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192785.

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There is considerable interest in how cells respond to mechanical stimuli, from the ligands used to transmit the stimulus to the signaling pathways initiated and the proteins expressed upon phenotype change [1]. Previous work focused on the evaluation of the quality of the extracellular matrix (ECM) coating and cell proliferation [2]. Our focus is the characterization of a flexible polymeric substrate, treated with ECM, used to induce tensile strain on cells. In this work, we expand our physical characterization of the protein modified polydimethylsiloxane (PDMS) surface by quantifying the cov
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Reports on the topic "Protein; Ligands"

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Lehnert, B., and D. Allen. Targeted in vitro evolution of protein ligands. Office of Scientific and Technical Information (OSTI), 2000. http://dx.doi.org/10.2172/767437.

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Zhou, Xia-Ying. Effects of ancillary ligands on selectivity of protein labeling with platinum(II) chloro complexes. Office of Scientific and Technical Information (OSTI), 1990. http://dx.doi.org/10.2172/6941351.

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Shin, Seung-Uon. Antibody-NKG2D Ligand (Rae-1Beta) Fusion Protein for Breast Cancer Therapy. Defense Technical Information Center, 2005. http://dx.doi.org/10.21236/ada446435.

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Bartsch, Richard A. New Proton-Ionizable, Calixarene-Based Ligands for Selective Metal Ion Separations. Office of Scientific and Technical Information (OSTI), 2012. http://dx.doi.org/10.2172/1041406.

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Montal, Mauricio. Channel Protein Engineering: A Novel Approach towards the Molecular Dissection Determinants in Ligand-Regulated Channels. Defense Technical Information Center, 1990. http://dx.doi.org/10.21236/ada219134.

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Dmitriev, Igor P., and Elena A. Kashentseva. Targeting of Adenovirus Vectors to Breast Cancer Mediated by Soluble Receptor-Ligand Fusion Proteins. Defense Technical Information Center, 2002. http://dx.doi.org/10.21236/ada407364.

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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), 2000. http://dx.doi.org/10.2172/768788.

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