Relevant bibliographies by topics / Ligand-based design

Contents

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

Academic literature on the topic 'Ligand-based design'

Author: Grafiati
Published: 7 June 2025
Last updated: 2 August 2025

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Journal articles on the topic "Ligand-based design"

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Stalke, D. "Charge density based ligand design." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C69. http://dx.doi.org/10.1107/s010876730809778x.

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Kargbo, Robert B. "Ligand Design for Cereblon Based Immunomodulatory Therapy." ACS Medicinal Chemistry Letters 11, no. 6 (2020): 1088–89. http://dx.doi.org/10.1021/acsmedchemlett.0c00214.

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Joseph-McCarthy, D. "Computational approaches to structure-based ligand design." Pharmacology & Therapeutics 84, no. 2 (1999): 179–91. http://dx.doi.org/10.1016/s0163-7258(99)00031-5.

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Böhm, Hans-Joachim. "Computational tools for structure-based ligand design." Progress in Biophysics and Molecular Biology 66, no. 3 (1996): 197–210. http://dx.doi.org/10.1016/s0079-6107(97)00005-9.

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Barelier, Sarah, Julien Pons, Kalle Gehring, Jean-Marc Lancelin, and Isabelle Krimm. "Ligand Specificity in Fragment-Based Drug Design." Journal of Medicinal Chemistry 53, no. 14 (2010): 5256–66. http://dx.doi.org/10.1021/jm100496j.

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Katz, Bradley A., Robert T. Cass, Beishan Liu, Rafael Arze, and Nathan Collins. "Topochemical Catalysis Achieved by Structure-based Ligand Design." Journal of Biological Chemistry 270, no. 52 (1995): 31210–18. http://dx.doi.org/10.1074/jbc.270.52.31210.

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Clark, David. "Ligand-based drug design in the AlphaFold age." Biomedical & Life Sciences Collection 2025, no. 6 (2025): e1006819. https://doi.org/10.69645/biuu5747.

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Apostolakist, J., and A. Caflisch. "Computational Ligand Design." Combinatorial Chemistry & High Throughput Screening 2, no. 2 (1999): 91–104. http://dx.doi.org/10.2174/1386207302666220203193501.

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Abstract: A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug­ like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative st
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Douguet, Dominique, Hélène Munier-Lehmann, Gilles Labesse, and Sylvie Pochet. "LEA3D: A Computer-Aided Ligand Design for Structure-Based Drug Design." Journal of Medicinal Chemistry 48, no. 7 (2005): 2457–68. http://dx.doi.org/10.1021/jm0492296.

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Wilson, Gregory L., and Markus A. Lill. "Integrating structure-based and ligand-based approaches for computational drug design." Future Medicinal Chemistry 3, no. 6 (2011): 735–50. http://dx.doi.org/10.4155/fmc.11.18.

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Dissertations / Theses on the topic "Ligand-based design"

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Boas, F. Edward. "Physics-based design of protein-ligand binding /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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Hevener, Kirk Edward. "Structure- and ligand-based design of novel antimicrobial agents." View the abstract Download the full-text PDF version, 2008. http://etd.utmem.edu/ABSTRACTS/2008-052-Hevener-index.htm.

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Thesis (Ph.D.)--University of Tennessee Health Science Center, 2008.<br>Title from title page screen (viewed on February 2, 2009). Research advisor: Richard E. Lee, Ph.D. Document formatted into pages (xviii, 238 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 167-186).
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Kekenes-Huskey, Peter Michael Heath James R. Goddard William A. "A Monte Carlo-based torsion construction algorithm for ligand design /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-05282009-131419.

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Nilapwar, S. "Characterization and exploitation of protein ligand interactions for structure based drug design." Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/19034/.

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Most characterised protein-small molecule interactions that display a change in heat capacity (\bigtriangleupCp) occur with a negative \bigtriangleupCp value. This is often attributed to solvent reorganisation from reduction in solvent accessible apolar surface area accompanying complex formation. Positive \bigtriangleupCp values have not been widely reported and could typically be attributed to an increased solvent accessible apolar surface area, desolvation of polar surface area or structural transitions in the biomolecular complex. Heat shock protein-90 (Hsp90) is one of the abundant and im
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Schulz, Michèle Nadine. "Fragment based ligand discovery : library design and screening by thermal shift analysis." Thesis, University of York, 2012. http://etheses.whiterose.ac.uk/3133/.

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The central idea in Fragment Based Ligand Discovery (FBLD) is to identify small, low molecular weight compounds (MW < 250) that bind to a particular protein active site. Hits can be used to efficiently design larger compounds with the desired affinity and selectivity. Three approaches to FBLD are described in this thesis. The first topic is the development and assessment of different chemoinformatics procedures to select those fragments that maximally represent the chemical features of a larger compound library. Such a fragment library could be of great value in the so-called “SAR by Catalogue
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Speidel, Joshua A. "Computational approaches to structure based ligand design : an illustration for P/CAF bromodomain ligands /." Access full-text from WCMC, 2007. http://proquest.umi.com/pqdweb?did=1453183061&sid=21&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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Tai, Hio Kuan. "Protein-ligand docking and virtual screening based on chaos-embedded particle swarm optimization algorithm." Thesis, University of Macau, 2018. http://umaclib3.umac.mo/record=b3948431.

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Müskens, Frederike Maximiliane. "Design, synthesis and evaluation of a molecular probe for ligand-based receptor capture targeting membrane receptors." Thesis, University of Glasgow, 2019. http://theses.gla.ac.uk/40984/.

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Membrane proteins are vital to drug discovery, being targeted by some 60% of the currently marketed therapeutic medicines, with more than half of those targeting transmembrane receptors. Identification of transmembrane receptor targets of poorly characterised ligands can provide new starting points for drug innovation, provide valuable information about off-target effects, and enhance mechanistic understanding of molecular pathways. Whereas, over the years, various methods for target identification have been developed, due to unfavourable characteristics, such as hydrophobicity, low abundance
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Li, Huameng. "Multiple Ligand Simultaneous Docking (MLSD) and Its Applications to Fragment Based Drug Design and Drug Repositioning." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1324606149.

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Spink, Ian. "Ligand discovery for protein-protein interaction targets using 19F NMR-based screening of novel peptide and fragment libraries." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31536.

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The main aim of this thesis was to discover and design new ligands for difficult, under-explored and clinically relevant protein targets. A number of protein-protein interaction complexes (PPIs) are introduced as the target focus for the methods employed and developed herein. This thesis is separated into two sections to independently address both peptides and small molecules as screening agents. The project examines both approaches through comprehensive library design strategies and screening by NMR spectroscopic methods. ATAD2 is the first PPI investigated and was expressed and purified in g
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Books on the topic "Ligand-based design"

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Hans-Joachim, Böhm, and Gubernator Klaus, eds. Structure-based ligand design. Wiley-VCH, 1998.

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1959-, Merz Kenneth M., Ringe Dagmar, and Reynolds Charles H. 1957-, eds. Drug design: Structure and ligand-based approaches. Cambridge University Press, 2010.

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Merz, Kenneth M. Drug design: Structure- and ligand-based approaches. Cambridge University Press, 2010.

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Mannhold, Raimund, Hugo Kubinyi, Hendrik Timmerman, Hans-Joachim B�hm, and Klaus Gubernator. Structure-Based Ligand Design. Wiley & Sons, Incorporated, John, 2008.

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Gubernator, Klaus, and Hans‐Joachim Böhm, eds. Structure-Based Ligand Design. Wiley, 1998. http://dx.doi.org/10.1002/9783527612178.

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Mannhold, Raimund, Hugo Kubinyi, Hendrik Timmerman, Hans-Joachim B�hm, and Klaus Gubernator. Structure-Based Ligand Design. Wiley & Sons, Limited, John, 2008.

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Kenneth M. Merz Jr PhD, Dagmar Ringe PhD, and Charles H. Reynolds PhD. Drug Design: Structure- and Ligand-Based Approaches. Cambridge University Press, 2010.

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Reynolds, Charles H., Dagmar Ringe, and Kenneth M. Merz. Drug Design: Structure- and Ligand-Based Approaches. Cambridge University Press, 2010.

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Reynolds, Charles H., Dagmar Ringe, and Merz Kenneth M. Jr. Drug Design: Structure- and Ligand-Based Approaches. Cambridge University Press, 2010.

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Reynolds, Charles H., Dagmar Ringe, and Merz Kenneth M. Jr. Drug Design: Structure- and Ligand-Based Approaches. Cambridge University Press, 2006.

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Book chapters on the topic "Ligand-based design"

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Gubernator, K., C. Broger, D. Bur, et al. "Structure-Based Ligand Design." In Computer Aided Drug Design in Industrial Research. Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-662-03141-4_4.

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Fayne, Darren. "Ligand-Based Molecular Design Using Pseudoreceptors." In De novo Molecular Design. Wiley-VCH Verlag GmbH & Co. KGaA, 2013. http://dx.doi.org/10.1002/9783527677016.ch9.

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Palazzesi, Ferruccio, and Alfonso Pozzan. "Deep Learning Applied to Ligand-Based." In Artificial Intelligence in Drug Design. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1787-8_12.

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Söderhjelm, Pär, Samuel Genheden, and Ulf Ryde. "Quantum Mechanics in Structure-Based Ligand Design." In Protein-Ligand Interactions. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch7.

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Aberer, Karl, Klemens Hemm, and Manfred Hendlich. "Data Management for Ligand-Based Drug Design." In Theoretical and Computational Methods in Genome Research. Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-5903-0_16.

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Abdo, Ammar, and Naomie Salim. "Ligand-Based Virtual Screening Using Bayesian Inference Network." In Library Design, Search Methods, and Applications of Fragment-Based Drug Design. American Chemical Society, 2011. http://dx.doi.org/10.1021/bk-2011-1076.ch004.

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van der Sloot, Almer M., and Wim J. Quax. "Computational Design of TNF Ligand-Based Protein Therapeutics." In Advances in Experimental Medicine and Biology. Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-6612-4_54.

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Schneider, Gisbert, and Petra Schneider. "Coping with Complexity in Ligand-Based De Novo Design." In Frontiers in Molecular Design and Chemical Information Science - Herman Skolnik Award Symposium 2015: Jürgen Bajorath. American Chemical Society, 2016. http://dx.doi.org/10.1021/bk-2016-1222.ch008.

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Hawkins, Paul C. D., and Gunther Stahl. "Ligand-Based Methods in GPCR Computer-Aided Drug Design." In Methods in Molecular Biology. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7465-8_18.

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Boros, Eszter, Bernadette V. Marquez, Oluwatayo F. Ikotun, Suzanne E. Lapi, and Cara L. Ferreira. "Coordination Chemistry and Ligand Design in the Development of Metal Based Radiopharmaceuticals." In Ligand Design in Medicinal Inorganic Chemistry. John Wiley & Sons, Ltd, 2014. http://dx.doi.org/10.1002/9781118697191.ch3.

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Conference papers on the topic "Ligand-based design"

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Hussein, Layth, P. Ilanchezhian, Praveen Kumar Hiremath, V. Sivakumar, and S. Senthil Kumar. "Dual Channel based Convolutional Neural Network based Protein–Ligand Interaction Prediction for Drug Design." In 2024 First International Conference on Software, Systems and Information Technology (SSITCON). IEEE, 2024. https://doi.org/10.1109/ssitcon62437.2024.10796432.

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"Deep Belief Networks for Ligand-Based Virtual Screening of Drug Design." In 2016 the 6th International Workshop on Computer Science and Engineering. WCSE, 2016. http://dx.doi.org/10.18178/wcse.2016.06.115.

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Figuerola-Asencio, Laura, Paula Morales, Dow P. Hurst, et al. "Ligand-based drug design approaches for the identification of novel GPR55 modulators." In 6th International Electronic Conference on Medicinal Chemistry. MDPI, 2020. http://dx.doi.org/10.3390/ecmc2020-07487.

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Wahib, Mohamed, Asim Munawar, Masaharu Munetomo, and Kiyoshi Akama. "A Bayesian Optimization Algorithm for De Novo ligand design based docking running over GPU." In 2010 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2010. http://dx.doi.org/10.1109/cec.2010.5586531.

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Gracia, Luis. "New Computational Approaches for NMR-based Drug Design: A Protocol for Ligand Docking to Flexible Target Sites." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345634.

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Marzaro, Giovanni, and Carmen Di Giovanni. "A mixed ligand – Autogrid based pharmacophore model for the rational design of multi-kinase inhibitors ." In MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2nd edition. MDPI, 2016. http://dx.doi.org/10.3390/mol2net-02-01005.

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Mladenović, Milan P., Nevena M. Tomašević, Sanja Lj Matić, Tamara M. Mladenović, and Rino Ragno. "Computer-aided design of new drugs against breast cancer." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.641m.

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Computational medicinal chemistry, if used properly and in accordance with the available experimental data, may provide significant support to rational drug design. Herein, an overview of the computational approaches that have been applied to an estrogen receptor α (ERα) and endowed in the rational design of pM ERα antagonists with profound anti-breast cancer activity either in vitro or in vivo, will be presented. ERα is a 17β-estradiol inducible transcriptional regulator that initiates the RNA polymerase II-dependent transcriptional machinery, pointed for breast cancer (BC) development via ei
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Zuo, Lei, Xiaoming Chen, and Ming Lu. "Design and Fabrication of Differential Scanning Nanocalorimeter for Biological Applications." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-48704.

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This paper describes the design, fabrication, and characterization of a differential scanning nanocalorimeter that has potential to significantly reduce the sample volume to microliter and improve the temperature sensitivity to 10 μK. The nanocalorimeter consists of a polymeric freestanding membrane, four high-sensitive low-noise thermistors based on the silicon carbide (SiC), and a platinum heater and temperature sensor. With the integrated heater and sensors, temperature scanning and power compensation can be achieved for calorimetric measurement. Temperature sensing SiC film was prepared by
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Beljkas, Milan, Jelena Rebić, Milica Radan, Teodora Đikić, Slavica Oljačić, and Katarina Nikolic. "3D-Quantitative Structure-Activity Relationship and design of novel Rho-associated protein kinases-1 (ROCK1) inhibitors." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.584b.

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Rho-associated coiled-coil kinases (ROCKs) are involved in essential cellular functions such as adhesion, contraction, motility, proliferation, and cell survival/apoptosis. Four ROCK inhibitors have already been approved by the FDA and are used to treat glaucoma (ripasudil and netarsudil), cerebral vasospasm (fasudil), and graft-versus-host disease (belumosudil). Recent studies have focused on exploring the role of ROCK kinase inhibitors in cancer treatment and the development of new ROCK inhibitors. The main objective of this study was to identify critical structural features relevant to the
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Warsito, Warsito, Masruri Masruri, Sinta Murlistyarini, Dwika Putri Pangesti, and Asyfariatus Zulfa Azhar. "Screening Multitarget Anticancer Compounds from Salicylic Acid Derivatives: (Without and with Amino Acid Linkage) by <i>In Silico</i> Docking." In International Conference on Chemistry and Material Sciences 2023 (IC2MS). Trans Tech Publications Ltd, 2024. http://dx.doi.org/10.4028/p-svkm5p.

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This research aims to design anticancer molecules using the hybridization concept based on molecular derivatives of salicylic acid. The investigation explores structures with and without linked amino acid alanine through an in-silico docking approach. The research conducts screenings of the designed salicylic acid derivative molecules against receptors, including MMP9, MMP2, CDK2, P53, BAK EGFR, and ADP Ribose Polymerase. The most promising docking results for multitarget cancer compounds were observed in salicylic acid derivatives with amino acid linkages, specifically salicylic acid-curcumin
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Reports on the topic "Ligand-based design"

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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, 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 mut
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Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7593398.bard.

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The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist bioph
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Eyal, Yoram, and Sheila McCormick. Molecular Mechanisms of Pollen-Pistil Interactions in Interspecific Crossing Barriers in the Tomato Family. United States Department of Agriculture, 2000. http://dx.doi.org/10.32747/2000.7573076.bard.

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During the evolutionary process of speciation in plants, naturally occurring barriers to reproduction have developed that affect the transfer of genes within and between related species. These barriers can occur at several different levels beginning with pollination-barriers and ending with hybrid-breakdown. The interaction between pollen and pistils presents one of the major barriers to intra- and inter-specific crosses and is the focus of this research project. Our long-term goal in this research proposal was defined to resolve questions on recognition and communication during pollen-pistil
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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, 2006. http://dx.doi.org/10.32747/2006.7587235.bard.

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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and
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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial iden
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