Relevant bibliographies by topics / Structure- and fragment-based drug design

Contents

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

Academic literature on the topic 'Structure- and fragment-based drug design'

Author: Grafiati
Published: 5 June 2025
Last updated: 2 August 2025

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Journal articles on the topic "Structure- and fragment-based drug design"

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Bancet, Alexandre, Claire Raingeval, Thierry Lomberget, Marc Le Borgne, Jean-François Guichou, and Isabelle Krimm. "Fragment Linking Strategies for Structure-Based Drug Design." Journal of Medicinal Chemistry 63, no. 20 (2020): 11420–35. http://dx.doi.org/10.1021/acs.jmedchem.0c00242.

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Du, Qi-Shi, Ri-Bo Huang, Yu-Tuo Wei, Zong-Wen Pang, Li-Qin Du, and Kuo-Chen Chou. "Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design." Journal of Computational Chemistry 30, no. 2 (2009): 295–304. http://dx.doi.org/10.1002/jcc.21056.

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Mendes, Vitor, and Tom L. Blundell. "Targeting tuberculosis using structure-guided fragment-based drug design." Drug Discovery Today 22, no. 3 (2017): 546–54. http://dx.doi.org/10.1016/j.drudis.2016.10.003.

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Kashyap, Aanchal, Pankaj Kumar Singh, and Om Silakari. "Counting on Fragment Based Drug Design Approach for Drug Discovery." Current Topics in Medicinal Chemistry 18, no. 27 (2019): 2284–93. http://dx.doi.org/10.2174/1568026619666181130134250.

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Fragment based drug design (FBDD) is a structure guided ligand design approach used in the process of drug discovery. It involves identification of low molecular weight fragments as hits followed by determination of their binding mode using X-ray crystallography and/or NMR spectroscopy. X-ray protein crystallography is one of the most sensitive biophysical methods used for screening and is least prone to false positives. It also provides detailed structural information of the protein–fragment complex at the atomic level. The retrieved binding information facilitates the optimization of fragmen
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Zhang, Changsheng, and Luhua Lai. "Towards structure-based protein drug design." Biochemical Society Transactions 39, no. 5 (2011): 1382–86. http://dx.doi.org/10.1042/bst0391382.

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Structure-based drug design for chemical molecules has been widely used in drug discovery in the last 30 years. Many successful applications have been reported, especially in the field of virtual screening based on molecular docking. Recently, there has been much progress in fragment-based as well as de novo drug discovery. As many protein–protein interactions can be used as key targets for drug design, one of the solutions is to design protein drugs based directly on the protein complexes or the target structure. Compared with protein–ligand interactions, protein–protein interactions are more
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van Montfort, Rob L. M., and Paul Workman. "Structure-based drug design: aiming for a perfect fit." Essays in Biochemistry 61, no. 5 (2017): 431–37. http://dx.doi.org/10.1042/ebc20170052.

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Knowledge of the three-dimensional structure of therapeutically relevant targets has informed drug discovery since the first protein structures were determined using X-ray crystallography in the 1950s and 1960s. In this editorial we provide a brief overview of the powerful impact of structure-based drug design (SBDD), which has its roots in computational and structural biology, with major contributions from both academia and industry. We describe advances in the application of SBDD for integral membrane protein targets that have traditionally proved very challenging. We emphasize the major pro
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Murray, Christopher W., and Tom L. Blundell. "Structural biology in fragment-based drug design." Current Opinion in Structural Biology 20, no. 4 (2010): 497–507. http://dx.doi.org/10.1016/j.sbi.2010.04.003.

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Shulga, Dmitry A., Nikita N. Ivanov, and Vladimir A. Palyulin. "In Silico Structure-Based Approach for Group Efficiency Estimation in Fragment-Based Drug Design Using Evaluation of Fragment Contributions." Molecules 27, no. 6 (2022): 1985. http://dx.doi.org/10.3390/molecules27061985.

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The notion of a contribution of a specific group in an organic molecule’s property and/or activity is both common in our thinking and is still not strictly correct due to the inherent non-additivity of free energy with respect to molecular fragments composing a molecule. The fragment- based drug discovery (FBDD) approach has proven to be fruitful in addressing the above notions. The main difficulty of the FBDD, however, is in its reliance on the low throughput and expensive experimental means of determining the fragment-sized molecules binding. In this article we propose a way to enhance the t
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Pihan, Emilie, Lionel Colliandre, Jean-François Guichou, and Dominique Douguet. "e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design." Bioinformatics 28, no. 11 (2012): 1540–41. http://dx.doi.org/10.1093/bioinformatics/bts186.

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Malhotra, Sony, Sherine E. Thomas, Bernardo Ochoa Montano, and Tom L. Blundell. "Structure-guided, target-based drug discovery – exploiting genome information from HIV to mycobacterial infections." Postępy Biochemii 62, no. 3 (2016): 262–72. http://dx.doi.org/10.18388/pb.2016_25.

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The use of protein crystallography in structure-guided drug discovery allows identification of potential inhibitor-binding sites and optimisation of interactions of hits and lead compounds with a target protein. An early example of this approach was the use of the structure of HIV protease in designing AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design. Here, we discuss the use of structure-guided target identification and lead op
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Dissertations / Theses on the topic "Structure- and fragment-based drug design"

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Jayawickrama, Gayan. "Study and Design of Kynurenine Aminotransferase-II Inhibitors for the Treatment of Neurological Conditions." Thesis, The University of Sydney, 2018. http://hdl.handle.net/2123/20270.

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The majority of tryptophan metabolism passes through the kynurenine pathway. Metabolic imbalances in this pathway are implicated disease. KYNA, transaminated by the kynurenine aminotransferase (KAT) enzymes, is elevated in patients with schizophrenia. Schizophrenia is a neuropsychiatric disease with limited treatment options and debilitating symptoms. Glutamatergic systems are thought to have a significant role in its pathogenesis, providing a basis by which KYNA, an endogenous glutamate antagonist, is implicated in the disease. Four pyridoxal 5’-phosphate-dependent homologues of KAT are repor
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Guca, Ewelina. "Caractérisation structurale de la CTP : phosphocholine cytidylyltransférase de Plasmodium falciparum et identification de composés inhibiteurs basée sur la structure visant à cibler la voie de biosynthèse des phospholipides." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT077.

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À l’heure actuelle, le paludisme reste un problème de santé majeur et demeure une des maladies parasitaires les plus menaçantes. Parmi les cinq espèces de malaria infectant l’homme, Plasmodium falciparum est la forme la plus mortelle. Lors de la phase érythrocytaire de son cycle de vie, causant tous les symptômes du paludisme, P.falciparum utilise les phospholipides pour créer les membranes nécessaires au développement de cellules filles. Chez P. falciparum, la phosphatidylcholine est principalement obtenue grâce à la voie de synthèse de novo, dite voie de Kennedy. Dans cette voie de biosynthè
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Radoux, Christopher John. "The automatic detection of small molecule binding hotspots on proteins : applying hotspots to structure-based drug design." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/275133.

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Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods typically assess the pocket as a whole, doing little to suggest which regions and interactions are the most important for binding. This thesis introduces Fragment Hotspot Maps, a grid-based method that samples atomic propensities derived from interactions in the Cambridge Structural Database (CSD) with simple molecular probes. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores, offering more precision over other binding site prediction m
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Ward, Richard. "Targeting inositol monophosphatase in structure-based drug design." Thesis, University of Birmingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289291.

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Amadi, Cecilia Nwadiuto. "Biochemical and drug targeting studies of Mycobacterium tuberculosis cholesterol oxidase P450 enzymes." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/biochemical-and-drug-targeting-studies-of-mycobacterium-tuberculosis-cholesterol-oxidase-p450-enzymes(16cbca7a-b8b2-4ec4-bbd7-977785ed65b9).html.

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Mycobacterium tuberculosis (Mtb), a deadly pathogen, has scourged mankind for many centuries and has remained a major threat to global world health. Tuberculosis, the disease caused by this bacterium, is a major cause of death in developing nations and there is potential for its re-emergence in developed countries. An alarming rise in cases of multidrug-resistant and extremely-drug resistant tuberculosis (MDR-TB and XDR-TB) that do not respond to the customary first-line antibiotics necessitates the urgent need for development of new anti-TB drugs. Mtb becomes engulfed in human macrophages pos
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Mukherjee, Sreya. "Applications of Molecular Modelling and Structure Based Drug Design in Drug Discovery." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6331.

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Calcium ions have important roles in cellular processes including intracellular signaling, protein folding, enzyme activation and initiation of programmed cell death. Cells maintain low levels of calcium in their cytosol in order to regulate these processes. When activation of calcium-dependent processes is needed, cells can release calcium stored in the endoplasmic reticulum (ER) into the cytosol to initiate the processes. This can also initiate formation of plasma membrane channels that allow entry of additional calcium from the extracellular milieu. The change in calcium levels is referred
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Wang, Feng. "Structure-based drug mechanism study and inhibitor design targeting tuberculosis." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1439.

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Vankayala, Sai Lakshmana Kumar. "Computational Approaches for Structure Based Drug Design and Protein Structure-Function Prediction." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4601.

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This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kin
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Zephyr, Jacqueto. "Robust Drug Design Strategies and Discovery Targeting Viral Proteases." eScholarship@UMMS, 2021. https://escholarship.umassmed.edu/gsbs_diss/1157.

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Viral proteases play crucial roles in the life cycle and maturation of many viruses by processing the viral polyprotein after translation and in some cases cleaving host proteins associated with the immune response. The essential role of viral proteases makes them attractive therapeutic targets. In this thesis, I provide an introductory summary of viral proteases, their structure, mechanism, and inhibition, while the breadth of this thesis focuses on the Hepatitis C virus (HCV) NS3/4A and Zika virus (ZIKV) NS2B/NS3 viral proteases. HCV NS3/4A protease inhibitors (PIs) have become a mainstay in
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Rogers, Graeme W. "The development of sialidase inhibitors using structure-based drug design." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/15516.

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The sialidases/neuraminidases represent a family of enzymes whose function is important in the pathogenicity of bacteria and the virulence of influenza. Relenza and Tamiflu represent two drugs that were developed using structure-based drug design (SBDD) and computational-assisted drug design (CADD). These drugs target the active site of the influenza neuraminidase A and B (GH-34 family). Sialidases in the GH-33 family could represent novel drug targets for the treatment of bacterial or parasitic infection. SBDD was employed to develop chemical tools of two GH-33 sialidases, NanB and TcTS. NanB
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Books on the topic "Structure- and fragment-based drug design"

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Codding, Penelope W., ed. Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0.

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Pandi, Veerapandian, ed. Structure-based drug design. Marcel Dekker, 1997.

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Marti, Marcelo A., Adrian Gustavo Turjanski, and Dario Fernández Do Porto, eds. Structure-Based Drug Design. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-69162-1.

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Harren, Jhoti, and Leach Andrew R, eds. Structure-based drug discovery. Springer, 2007.

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

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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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W, Codding Penelope, North Atlantic Treaty Organization. Scientific Affairs Division., and NATO Advanced Study Institute on Experimental and Computational Approaches to Structure-Based Drug Design (1996 : Erice, Italy), eds. Structure-based drug design: Experimental and computational approaches. Kluwer Academic Publishers, 1998.

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Ward, Richard Andrew. Targeting Inositol Monophosphatase in structure-based drug design. University of Birmingham, 2002.

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1960-, Ladbury John E., and Connelly Pat R. 1961-, eds. Structure-based drug design: Thermodynamics, modeling, and strategy. Landes Bioscience, 1997.

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Du, Qishi. Developments in structure-based theoretical modeling of hydrophobicity for computer-aided drug design. Laurentian University Press, 1995.

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Book chapters on the topic "Structure- and fragment-based drug design"

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Atmakuri, Lakshmana Rao, Raveesha Peeriga, Gope Edward Raju, Srikanth Pottendla, Marapatla Shiny, and Amala Masa. "Structure-Based Drug Design and Fragment-Based Drug Discovery." In Innovations in Drug Discovery. Routledge, 2025. https://doi.org/10.4324/9781003564041-5.

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Ozawa, Tomonaga, Kosuke Okazaki, and Motohiro Nishio. "FMO as a Tool for Structure-Based Drug Design." In The Fragment Molecular Orbital Method. CRC Press, 2009. http://dx.doi.org/10.1201/9781420078497-11.

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Qu, Kunbin, and Natasja Brooijmans. "Structure-Based Drug Design." In Computational Methods for Protein Structure Prediction and Modeling. Springer New York, 2007. http://dx.doi.org/10.1007/978-0-387-68825-1_5.

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Duax, W. L., and J. F. Griffin. "Steroid Hormone Structure, Receptor Binding and Activity: Empirical Drug Design." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_1.

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Benedetti, Ettore, Rosa Iacovino, and Michele Saviano. "The Use of Uncoded α-Amino Acids Residues in Drug Design." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_10.

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Cole, Jason C., Jos P. M. Lommerse, R. Scott Rowland, Robin Taylor, and Frank H. Allen. "Use of the Cambridge Structural Database to Study Non-Covalent Interactions: Towards a Knowledge Base of Intermolecular Interactions." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_11.

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Pauptit, Richard, Simon Weston, Siân Rowsell, Dean Derbyshire, and Alec Tucker. "Immunoconjugates as Anti-Cancer Agents." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_12.

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Hendrickson, Thomas F., and Lana Schaffer. "Database Searching using Protein Crystal Structures and Molecular Docking Procedures." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_13.

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King, Ross D., Michael J. E. Sternberg, Stephen H. Muggleton, and Ashwin Srinivasan. "Recent Developments in Applying Machine Learning to Drug Design." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_14.

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Grootenhuis, Peter D. J., and Constant A. A. Boeckel. "Structure-Based Design of Novel Heparin-Like Anticoagulants." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_15.

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Conference papers on the topic "Structure- and fragment-based drug design"

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Chaudhary, Shashank, Devyani Chudasama, Jaiprakash Verma, and Swati Jain. "Analysing Scoring Functions for Molecular Structure-based Drug Design." In 2024 First International Conference on Technological Innovations and Advance Computing (TIACOMP). IEEE, 2024. http://dx.doi.org/10.1109/tiacomp64125.2024.00036.

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Tyrell, Stacey, Mark Robeson, Courtney Kube, Dennis McCarthy, and Ronald Lavin. "Dual-Use Structures: Composite Wing with Structural Antenna Aperture." In Vertical Flight Society 72nd Annual Forum & Technology Display. The Vertical Flight Society, 2016. http://dx.doi.org/10.4050/f-0072-2016-11552.

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Many modern aircraft, including rotorcraft, require conformal antennas and fairings to reduce wind drag, ice accretion, lightning strikes, and impact damage. An innovative composite wing configuration with a structural Ultra High Frequency (UHF) antenna window "aperture" has been developed. The wing is based on variants of lightweight X-Cor® sandwich core technology for durability and damage tolerance, with tailored electromagnetic properties in the aperture region of the wing. This paper presents a brief introduction to helicopter wings, a summary of recent research at Boeing and Army leading
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Selboe, G., H. Osvoll, and L. Brattas. "Optimizing of Corrosion Protection Based on a Combination of Cathodic Protection (CP) and Coating." In CORROSION 2004. NACE International, 2004. https://doi.org/10.5006/c2004-04097.

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Abstract When cathodically protecting a structure with sacrificial anodes, the required anode weight will decrease if the structure additionally is coated. For a lot of structures, reduction in weight is an important factor. It is important to reduce the lift weight for installation purposes and for design purposes it is important to reduce drag forces. Coating in combination with cathodic protection doesn't mean that the structure has to be 100% coated. By coating 90% of the surface areas, the anode weight may be reduced dramatically. This means that welding zones and damage to coating system
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Barhate, Yash, Daniel Casas-Orozco, Daniel J. Laky, Gintaras V. Reklaitis, and Zoltan K. Nagy. "Hybrid Rule-based and Optimization-driven Decision Framework for the Rapid Synthesis of End-to-End Optimal (E2EO) and Sustainable Pharmaceutical Manufacturing Flowsheets." In Foundations of Computer-Aided Process Design. PSE Press, 2024. http://dx.doi.org/10.69997/sct.115998.

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In this paper, a hybrid heuristic rule-based and deterministic optimization-driven process decision framework is presented for the analysis and optimization of process flowsheets for end-to-end optimal (E2E0) pharmaceutical manufacturing. The framework accommodates various operating modes, such as batch, semi-batch and continuous, for the different unit operations that implement each manufacturing step. To address the challenges associated with solving process synthesis problems using a simulation-optimization approach, heuristic-based process synthesis rules are employed to facilitate the red
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Batista, Daniel V., and Marco S. Reis. "Balancing modelling complexity and experimental effort for conducting QbD on lipid nanoparticles (LNPs) systems." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.163183.

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The promising properties of lipid nanoparticles (LNPs) as drug carriers have been attracting significant attention in the field of drug delivery. However, further research is still required for a better understanding of their integration in the pharmaceutical industry. The Quality by Design (QbD) approach aims at ensuring the safety and efficiency in the development of new drugs, through an holistic, risk-based approach that gathers all sources of knowledge available about the system under analysis. One key resource of the QbD framework is the rich toolkit of Design of Experiments (DOE), to de
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Park, Seongjoong, Jinwhuy Lee, Jeonguk Choi, et al. "Aerodynamic Optimization for Rotor Blade with Structural Design in Hover and Forward Flight." In Vertical Flight Society 81st Annual Forum and Technology Display. The Vertical Flight Society, 2025. https://doi.org/10.4050/f-0081-2025-70.

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This study presents an integrated optimization framework for rotor blade design that combines aerodynamic shape optimization and internal structural design within a unified multidisciplinary process. A variable fidelity modeling (VFM) approach is employed to efficiently optimize the blade outer geometry for improved figure of merit (FM) in hover and lift-to-drag ratio (L/Dq) in forward flight. Based on the optimized aerodynamic shapes, internal structural optimization is subsequently performed using a surrogate model for predicting cross-sectional properties, ensuring dynamic feasibility while
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Houston, Douglas R., Ian Eggleston, Martin G. Peter, Bjornar Synstad, Vincent G. H. Eijsink, and Daan M. F. van Aalten. "CHITINASES - REACTION MECHANISM AND STRUCTURE-BASED DRUG DESIGN." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.472.

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Barrett, Kayleigh, Samantha Michaels, Edelmar Navaluna, et al. "P316 Structure-based drug design forneisseria gonorrhoeae, chlamydia trachomatis,andmycoplasma genitalium." In Abstracts for the STI & HIV World Congress (Joint Meeting of the 23rd ISSTDR and 20th IUSTI), July 14–17, 2019, Vancouver, Canada. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/sextrans-2019-sti.427.

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Unterlass, Judith E., Nabila Aljufri, Sophie Bex, Celine Cano, Martin E. M. Noble, and Nicola J. Curtin. "Abstract 2448: Towards structure-based drug design of 3-phosphoglycerate dehydrogenase inhibitors." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2448.

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Babu, M. Naresh, R. Bhramaramba, and Allam Appa Rao. "Structure based drug design studies on urokinase plasminogen activator inhibitors using AutoDock." In the Second International Conference. ACM Press, 2012. http://dx.doi.org/10.1145/2393216.2393301.

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Reports on the topic "Structure- and fragment-based drug design"

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DeLucas, Lawrence J. Crystallization, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes. Defense Technical Information Center, 1998. http://dx.doi.org/10.21236/ada360337.

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Trim, M., Matthew Murray, and C. Crane. Modernization and structural evaluation of the improved Overhead Cable System. Engineer Research and Development Center (U.S.), 2021. http://dx.doi.org/10.21079/11681/40025.

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A modernized Overhead Cable System prototype for a 689 ft (210 m) Improved Ribbon Bridge crossing was designed, assembled, and structurally tested. Two independent structural tests were executed, i.e., a component-level compression test of the BSS tower was performed to determine its load capacity and failure mode; and a system-level ‘dry’ test of the improved OCS prototype was conducted to determine the limit state and failure mode of the entire OCS. In the component-level compression test of the BSS tower, the compressive capacity was determined to be 102 kips, and the failure mode was local
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