Relevant bibliographies by topics / Structure-activity relationship (Biochemistry)

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Academic literature on the topic 'Structure-activity relationship (Biochemistry)'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Structure-activity relationship (Biochemistry)"

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Wawer, Mathias J., David E. Jaramillo, Vlado Dančík, Daniel M. Fass, Stephen J. Haggarty, Alykhan F. Shamji, Bridget K. Wagner, Stuart L. Schreiber, and Paul A. Clemons. "Automated Structure–Activity Relationship Mining." Journal of Biomolecular Screening 19, no. 5 (April 7, 2014): 738–48. http://dx.doi.org/10.1177/1087057114530783.

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Understanding the structure–activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.
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Hu, J. P., M. Calomme, A. Lasure, T. De Bruyne, L. Pieters, A. Vlietinck, and D. A. Vanden Berghe. "Structure-activity relationship of flavonoids with superoxide scavenging activity." Biological Trace Element Research 47, no. 1-3 (January 1995): 327–31. http://dx.doi.org/10.1007/bf02790134.

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Nagamurthi, G., and S. Rambhav. "Gramicidin-S: Structure-activity relationship." Journal of Biosciences 7, no. 3-4 (June 1985): 323–29. http://dx.doi.org/10.1007/bf02716794.

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Ávila, Hugo Pereira, Elza de Fátima Albino Smânia, Franco Delle Monache, and Artur Smânia. "Structure–activity relationship of antibacterial chalcones." Bioorganic & Medicinal Chemistry 16, no. 22 (November 2008): 9790–94. http://dx.doi.org/10.1016/j.bmc.2008.09.064.

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Bonafoux, Dominique F., Sheri L. Bonar, Michael Clare, Ann M. Donnelly, Jeanette L. Glaenzer, Julia A. Guzova, He Huang, et al. "Aminopyridinecarboxamide-based inhibitors: Structure–activity relationship." Bioorganic & Medicinal Chemistry 18, no. 1 (January 2010): 403–14. http://dx.doi.org/10.1016/j.bmc.2009.10.040.

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Shih-Fong, Chen, Lisa M. Papp, Robert J. Ardecky, Ganti V. Rao, David P. Hesson, Martin Forbes, and Daniel L. Dexter. "Structure-activity relationship of quinoline carboxylic acids." Biochemical Pharmacology 40, no. 4 (August 1990): 709–14. http://dx.doi.org/10.1016/0006-2952(90)90305-5.

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Ma, Anqi, Wenyu Yu, Yan Xiong, Kyle V. Butler, Peter J. Brown, and Jian Jin. "Structure–activity relationship studies of SETD8 inhibitors." MedChemComm 5, no. 12 (2014): 1892–98. http://dx.doi.org/10.1039/c4md00317a.

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Desai, A., C. Lee, L. Sharma, and A. Sharma. "Lysozyme refolding with cyclodextrins: structure–activity relationship." Biochimie 88, no. 10 (October 2006): 1435–45. http://dx.doi.org/10.1016/j.biochi.2006.05.008.

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Deng, Lisheng, Zana Muhaxhiri, Mary K. Estes, Timothy Palzkill, B. V. Venkataram Prasad, and Yongcheng Song. "Synthesis, activity and structure–activity relationship of noroviral protease inhibitors." MedChemComm 4, no. 10 (2013): 1354. http://dx.doi.org/10.1039/c3md00219e.

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Tsukano, Chihiro, and Makoto Sasaki. "Structure–activity relationship studies of gymnocin-A." Tetrahedron Letters 47, no. 38 (September 2006): 6803–7. http://dx.doi.org/10.1016/j.tetlet.2006.07.081.

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Dissertations / Theses on the topic "Structure-activity relationship (Biochemistry)"

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Nahas, Roger I. "Synthesis and structure-activity relationship of a series of sigma receptor ligands." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4840.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 26, 2008) Vita. Includes bibliographical references.
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Lanevskij, Kiril. "Absorption and Tissue Distribution of Drug-Like Compounds: Quantitative Structure-Activity Relationship Analysis." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2011. http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20111003_114235-89858.

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The objective of this work was to develop mechanistic quantitative structure activity relationship models that would facilitate the assessment of drug properties related to their absorption and distribution in the body. The analysis involved several parameters reflecting the rate of passive diffusion across brain endothelium and intestinal epithelium, and thermodynamic constants related to drug distribution between plasma and tissues. Permeation through cellular transport barriers was modeled by nonlinear equations relating the passive diffusion rate to physicochemical properties of drugs: lipophilicity, ionization, hydrogen bonding potential and molecular size. It was demonstrated that brain endothelium and intestinal epithelium exhibit a quantitatively similar pattern of permeability-ionization dependence – ionized species permeate 2-3 orders of magnitude slower than neutral molecules. Analysis of tissue to plasma partitioning data revealed the necessity to split original experimental values into separate terms reflecting plasma and tissue binding strength. Drugs’ affinity to tissues could then be described by their lipophilicity, whereas detrimental effect of ionization was only observed for acidic drugs. Finally, it was shown that a linear combination of quantitative blood-brain barrier transport parameters allows classifying drugs according to their access to central nervous system with 94% overall accuracy.
Šiame darbe pristatomi mechanistiniai kiekybinio struktūros ir aktyvumo ryšio modeliai, skirti vaistinių junginių savybių, charakterizuojančių jų absorbciją ir pasiskirstymą organizme prognozavimui. Nagrinėjama keletas parametrų, apibūdinančių paprastos difuzijos per biologines membranas greitį, taip pat termodinaminės konstantos, aprašančios vaistų pasiskirstymą tarp kraujo plazmos ir audinių. Ląstelinių pernašos barjerų pralaidumas buvo modeliuojamas netiesinėmis lygtimis, siejančiomis paprastos difuzijos greitį su vaistų fizikocheminėmis savybėmis, tokiomis kaip lipofiliškumas, jonizacija, vandenilinių ryšių sudarymo potencialas ir molekulių dydis. Nustatyta, kad smegenų endotelyje ir žarnyno epitelyje stebima panašaus pobūdžio difuzijos greičio priklausomybė nuo jonizacijos – katijonai ir anijonai difunduoja atitinkamai 2 ir 3 eilėmis lėčiau už neutralias molekules. Pademonstruota, kad analizuojant vaistų pasiskirstymo tarp audinių ir kraujo duomenis, būtina paversti pradines eksperimentines vertes kitais dydžiais, atspindinčiais vaistų jungimosi prie plazmos ir audinių komponentų stiprumą. Vaistų giminingumas audiniams gali būti aprašytas jų lipofiliškumu, o neigiama jonizacijos įtaka stebima tik rūgštiniams junginiams. Taip pat parodyta, kad vaistų pernašos per hematoencefalinę užtvarą kiekybinių parametrų tiesinė kombinacija leidžia 94% tikslumu klasifikuoti vaistus pagal jų prieinamumą centrinei nervų sistemai.
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DeBord, Michael. "Synthesis, characterization, and anti-cancer structure-activity relationship studies of imidazolium salts." University of Akron / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=akron1489414733025495.

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Pandit, Bulbul. "Study of structure activity relationship of analogs derived from SU-5416 and thalidomide and mechanism of antiproliferative activity." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187127289.

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Azizeh, Bassem Yousef. "Structure-activity relationship analysis: Developing glucagon agonists and antagonists for studies of glucagon action in normal and diabetic states." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/282252.

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Several glucagon analogues containing substitutions in the N-terminal region, in particular residues 1, 5, 6, 9 and 10 (histidine, threonine, phenylalanine, aspartic acid and tyrosine, respectively), were synthesized. In addition four β-methylphenylalanine isomers were introduced at position ten to assess the role of these topographical modifications on hormone activity, and to study the effect of constraint and biased conformational preferences of the side chain moieties on biological activity. All the analogues were synthesized by solid-phase methodology, purified to homogeneity by reverse-phase high-performance liquid chromatography, and characterized by electrospray mass spectroscopy, amino acid analysis and thin layer chromatography. Following characterization they were analyzed using rat liver plasma membranes for receptor-binding affinity as well as their ability to stimulate adenylate cyclase. Structure-activity relationship analysis provided critical information about the conformational, chemical and structural properties of amino acid residues required for receptor recognition and signal transduction in the glucagon sequence. His¹ was confirmed to operate along with Asp⁹ for the activation and binding to the glucagon receptor. These new findings should permit the design of more pure and potent glucagon receptor antagonists by focusing on the role of Phe⁶ and other residues in the N-terminal region. A newly developed assay for examining low levels of cAMP accumulation in response to glucagon antagonists, agonists and partial agonists was developed. Previously reported glucagon receptor antagonists had partial agonist activity in rat hepatocytes. This assay system, in conjunction with binding and adenylate cyclase studies in both hepatocytes and liver plasma membranes, redefines the major characteristics of pure glucagon antagonists. The most potent glucagon receptor antagonist [des-His¹, des-Phe⁶, Glu⁹]glucagon-NH₂ was studied using conformational analysis and 2D NMR techniques to analyze the secondary structure of the analogue. Proton resonance assignments using COSY, NOESY and TOCSY in d₆-DMSO were made.
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Hall, Sara M. "Bradykinin Ligands and Receptors Involved in Neuropathic Pain." Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/578606.

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Neuropathic pain is a prevalent disease with no effective, safe treatments and limited knowledge on the mechanisms involved. One target for neuropathic pain treatment may be the blockade of Dynorphin A (Dyn A). Dyn A is a unique endogenous ligand that possesses well-known neuroinhibitory effects via opioid receptors and neuroexcitatory effects that are mediated through the bradykinin 2 receptors (B2Rs). Extensive SAR was carried out to develop a ligand for the blockade of the excitatory actions of Dyn A at the B2R. A lead ligand was able to block Dyn A-induced hyperalgesia in naïve animals and was effective in a neuropathic pain model. However, the ligand was susceptible to enzymatic degradation. In an effort to increase the stability, modifications of the ligand using non-natural amino acids were performed. Analogues substituted at or near the N-terminus with a D-isomer retained binding at the receptor as well as provided a large increase in stability. These ligands were also found to be non-toxic in a cell toxicity assay. Dyn A has been found to not activate the classical signaling of the B2R, PI hydrolysis or Ca²⁺ mobilization. In an effort to determine Dyn A's signaling, a study was done examining up-regulation of phosphorylated proteins. It was found that Dyn A did not activate; pERK, 7 PKC isoforms or PKA. A well known B2R antagonist, HOE140, was found to have low affinity at rat and guinea pig brain B2Rs but high affinity in the guinea pig ileum. Further examination revealed that this discrepancy in binding may arise from a different isoform of the B2R that has not been previously examined. To date, we have discovered Dyn A analogues that have high affinity for the B2R, are very stable, and have low toxicity. The signaling pathway is still not fully understood, but further studies are underway. Also, there is evidence that the B2R in which the analogues are interacting at may be a different form than what has previously been described. Targeting this different isoform of the B2R with our current stable ligands may provide beneficial therapeutics for the treatment of neuropathic pain without the cardiovascular liabilities.
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Andersson, Karl. "Characterization of Biomolecular Interactions Using a Multivariate Approach." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4322.

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Jennings, Megan Christina. "Bioorganic Investigation of Quaternary Ammonium Compounds: Probing Antibacterial Activity and Resistance Development with Diverse Polyamine Scaffolds." Diss., Temple University Libraries, 2017. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/434038.

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Chemistry
Ph.D.
Quaternary ammonium compounds (QACs) have long served as lead disinfectants in residential, industrial, and hospital settings. Their simple yet effective amphiphilic nature makes them an ideal class of compounds through which to explore antibacterial activity. We have developed novel multiQAC scaffolds through simple and cost-efficient syntheses, yielding hundreds of diverse compounds strategically designed to examine various aspects of antibacterial and anti-biofilm activity, as well as toxicity. Many of these bis-, tris-, and tetraQACs display antibacterial activity 10 to 100 times greater than conventional monoQACs, and are among the most potent biofilm eradicators to date. Through analyzing their activity against several strains, we have uncovered and provided further evidence for key tenets of amphiphilic QAC bioactivity: a balance of hydrophobic side chains with cationic head groups generates optimal antibacterial activity, though toxicity to eukaryotic cells needs to be mitigated. Given their ubiquitous nature and chemical robustness, the overuse of QACs has led to the development of QAC resistance genes that are spreading throughout the microbial world at an alarming rate. These resistant strains, when found in bacterial biofilms, are able to persist in the presence of lead commercial QAC disinfectants, warranting the development of next-generation biocides. Several of our scaffolds were designed with QAC resistance machinery in mind; thus, we utilized these compounds not only as antibacterial agents but also as chemical probes to better understand and characterize QAC-resistance in methicillin-resistant Staphylococcus aureus (MRSA). Our findings support previous postulations that triscationic QACs would retain potency against QAC-resistant strains. Furthermore, we have identified monocationic and aromatic moieties, as well as conformational rigidity, as being more prone to recognition by the resistance machinery. Using our chemical toolbox comprised of QACs of various charge state and scaffold, we explored both the mechanism and scope of QAC-resistance by examining their structure-resistance relationship. Our holistic findings have allowed us to better understand the dynamics of this system towards the design and development of next-generation QACs that will: (1) allow us to better probe the resistance machinery, and (2) remain efficacious against a variety of microbial pathogens.
Temple University--Theses
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Goff, Randal Donald. "Structure-Activity Studies of Glycosphingolipids as Antigens of Natural Killer T Cells." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/942.

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Glycosphingolipids (GSLs), composed of a polar saccharide head and a lipophilic ceramide tail, are ubiquitous components of the plasma membrane of eukaryotic cells. They serve in many regulatory capacities and have antigenic properties towards natural killer T (NKT) cells of the innate immune system. Critical to the recognition of glycosylceramides by NKT cells are antigen presenting cells (APC), such as dendritic cells, which are responsible for binding, processing, and delivery of ligands to these lymphocytes. This event is mediated by CD1d, a major histocompatibility complex-like protein expressed on the surface of APCs, which binds GSL antigens by the ceramide moiety and presents the polar group to the T cell receptors of CD1d-restricted cells. The subsequent immune response involves NKT cell proliferation and emission of numerous cytokines, such as interferon-gamma (IFN-gamma) and interleukin-4 (IL-4), resulting in the stimulation of the innate and adaptive immune systems through maturation of APCs, activation of T cells, and secretion of antibodies by B cells. To understand the structure-activity relationship between GSLs and NKT cell activity and the requirements for intracellular processing of antigens, analogs of the model compound alphaGalCer (KRN-7000) have been synthesized. These include fluorophore-appended 6”-amino-α-galactosylceramides and N-alkenoyl GSLs, such as PBS-57, a potent alphaGalCer surrogate useful in NKT cell stimulation studies. A nonantigenic beta-C-galactosylceramide has also been prepared as an inhibitor of these innate lymphocytes. To probe the potential for using NKT cells to bias the immune system between the proinflammatory TH1 response or the immunomodulatory TH2 mode, versions of alphaGalCer with shortened ceramides have been created. One of these truncated analogs, PBS-25, has successfully been cocrystallized with CD1d and the binary complex structure solved by X-ray crystallography. Synthetic glycosphingolipids derived from Novosphingobium capsulatum and Sphingomonas paucimobilis have also been made. In assays with classical Valpha14i/Valpha24i NKT cell lines, these Gram-negative bacterial antigens were recognized directly and specifically by host immune systems through CD1d-restriction, unlike GSL-deficient microbes (e.g., Salmonella typhimurium). A search for other GSL-bearing alpha-proteobacteria led to the discovery of another natural glycosphingolipid, an N-alkenoylphytosphingoid-alpha-galactoside, isolated from the outer membrane of Ehrlichia muris.
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Trabbic, Christopher J. "Chemoenzymatic Synthesis of NAADP Derivatives: Probing the Unknown NAADP Receptor." University of Toledo Health Science Campus / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=mco1333749803.

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Books on the topic "Structure-activity relationship (Biochemistry)"

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1937-, Hall Lowell H., ed. Molecular connectivity in structure-activity analysis. Letchworth, Hertfordshire, England: Research Studies Press, 1986.

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1954-, Benner Steven A., and Schweizerischer Chemiker-Verband, eds. Redesigning the molecules of life: Conference papers of the International Symposium on Bioorganic Chemistry, Interlaken, May 4-6, 1988. Berlin: Springer-Verlag, 1988.

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Conversation in Biomolecular Stereodynamics (5th 1987 State University of New York at Albany). Structure & expression: Proceedings of the Fifth Conversation in the Discipline Biomolecular Stereodynamics held at the State University of New York at Albany, June 2-6, 1987. Schenectady, NY: Adenine Press, 1988.

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1939-, Sarma Ramaswamy H., and Sarma M. H. 1940-, eds. Structural biology: The state of the art : proceedings of the eighth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 22-26, 1993. Schenectady, N.Y: Adenine Press, 1994.

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D, Hegeman Adrian, ed. Enzymatic reaction mechanisms. New York: Oxford University Press, 2006.

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QSAR : Hansch analysis and related approaches. Weinheim: VCH, 1993.

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Martin, Yvonne Connolly. Quantitative drug design: A critical introduction. 2nd ed. Boca Raton, FL: Taylor & Francis, 2010.

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Martin, Yvonne Connolly. Quantitative drug design: A critical introduction. 2nd ed. Boca Raton: CRC Press/Taylor & Francis, 2010.

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Lin, Guo-Qiang. Chiral drugs: Chemistry and biological action. Hoboken, N.J: Wiley, 2011.

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Martin, Yvonne Connolly. Quantitative drug design: A critical introduction. 2nd ed. Boca Raton, FL: Taylor & Francis, 2010.

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Book chapters on the topic "Structure-activity relationship (Biochemistry)"

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Brandenburg, K., A. B. Schromm, and T. Gutsmann. "Endotoxins: Relationship Between Structure, Function, and Activity." In Subcellular Biochemistry, 53–67. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9078-2_3.

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Wenger, Roland M., Trevor G. Payne, and Max H. Schreier. "Cyclosporine: Chemistry, Structure-Activity Relationships and Mode of Action." In Progress in Clinical Biochemistry and Medicine, 157–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-70998-2_5.

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Fliri, Hans G., and Roland M. Wenger. "Chapter 10. Cyclosporine: Synthetic Studies, Structure- Activity Relationships, Biosynthesis and Mode of Action." In Biochemistry of Peptide Antibiotics, edited by Horst Kleinkauf and Hans von Döhren, 245–88. Berlin, Boston: De Gruyter, 1990. http://dx.doi.org/10.1515/9783110886139-011.

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Lorch, Mark. "3. Proteins." In Biochemistry: A Very Short Introduction, 34–51. Oxford University Press, 2021. http://dx.doi.org/10.1093/actrade/9780198833871.003.0003.

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This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.
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Katekar, Gerard F. "Structure-activity relationships of plant growth regulators." In Biochemistry and Molecular Biology of Plant Hormones, 89–111. Elsevier, 1999. http://dx.doi.org/10.1016/s0167-7306(08)60484-6.

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Zhao, Zheng, and Philip E. Bourne. "Using the Structural Kinome to Systematize Kinase Drug Discovery." In Biochemistry. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.100109.

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Kinase-targeted drug design is challenging. It requires designing inhibitors that can bind to specific kinases, when all kinase catalytic domains share a common folding scaffold that binds ATP. Thus, obtaining the desired selectivity, given the whole human kinome, is a fundamental task during early-stage drug discovery. This begins with deciphering the kinase-ligand characteristics, analyzing the structure–activity relationships and prioritizing the desired drug molecules across the whole kinome. Currently, there are more than 300 kinases with released PDB structures, which provides a substantial structural basis to gain these necessary insights. Here, we review in silico structure-based methods – notably, a function-site interaction fingerprint approach used in exploring the complete human kinome. In silico methods can be explored synergistically with multiple cell-based or protein-based assay platforms such as KINOMEscan. We conclude with new drug discovery opportunities associated with kinase signaling networks and using machine/deep learning techniques broadly referred to as structural biomedical data science.
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Blow, David. "Images and X-rays." In Outline of Crystallography for Biologists. Oxford University Press, 2002. http://dx.doi.org/10.1093/oso/9780198510512.003.0005.

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Crystallography provides the most direct way of forming images of molecules. Using crystallography, three-dimensional images have been made of thousands of macromolecules, especially proteins and nucleic acids. These give detailed information about their activity, their mechanism for recognizing and binding substrates and effectors, and the conformational changes which they may undergo. The three-dimensional structures show graphically the evolutionary relationships between molecules from widely separated systems. They give a wide view of the resemblances between different proteins, showing strong links in three-dimensional structure where the relationship between amino-acid sequences has dwindled to insignificance. The aim of this book is to tell the ordinary biologist enough about the methods of crystallography and the results that it gives, to allow results to be considered critically, to give insight into the limits of interpretation which are possible, and to identify the causes of the limitation in a particular case. Although the basic ideas are simple, the structural results are complicated, and based on huge numbers of measurements. The challenge for the teacher is to find a way through the simple basic ideas, without getting lost in detail. The main text is purely descriptive, and can be read from start to finish without any detailed mathematical knowledge. The explanations are backed up by numerous illustrations. For the reader who wants more detail, ‘boxes’ are supplied with more complete information, which can offer a deeper level of understanding, using some clearly presented mathematics. The book is not intended to teach the reader how to do practical crystallography. There are many other excellent books for this purpose. It is intended, rather, to give an overview which will allow any biochemist or molecular biologist to read structural papers with a critical awareness. In the first part of the book (Chapters 1–5), the general principles underlying the use of X-rays, crystals and diffraction are presented, using illustrations to make many of the ideas more graphic. In the second part (Chapters 6–13), the steps that need to be followed in the course of structure determination of a crystal are considered in more detail, again with many illustrations.
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