Relevant bibliographies by topics / In silico design

Contents

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

Academic literature on the topic 'In silico design'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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Journal articles on the topic "In silico design"

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DeWitt, Natalie. "In silico vaccine design?" Nature Biotechnology 17, no. 6 (1999): 523. http://dx.doi.org/10.1038/9813.

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Kotz, Joanne. "In silico drug design." Science-Business eXchange 6, no. 3 (2013): 50. http://dx.doi.org/10.1038/scibx.2013.50.

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Rees-Garbutt, Joshua, Jake Rightmyer, Jonathan R. Karr, Claire Grierson, and Lucia Marucci. "Furthering genome design using models and algorithms." Current Opinion in Systems Biology 24 (October 16, 2020): 120–26. https://doi.org/10.1016/j.coisb.2020.10.007.

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<strong>Highlights</strong> Models can investigate many more genome designs than laboratory research. Algorithms can search for genomes that optimise specific criteria. Together, models and algorithms can help engineers to design genomes. Algorithm-driven whole-cell model&nbsp;<em>in silico</em>&nbsp;designs could be viable&nbsp;<em>in&nbsp;vivo</em>. The genome design ecosystem needs improved modelling and design tools. <strong>Abstract</strong> Large-scale&nbsp;<em>in silico</em>&nbsp;genome designs are on the brink of being engineered&nbsp;<em>in&nbsp;vivo</em>, offering a potential paradig
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Triveni, S., C. Naresh Babu, E. Bhargav, and M. Vijaya Jyothi. "in silico Design, ADME Prediction, Molecular Docking, Synthesis of Novel Triazoles, Indazoles & Aminopyridines and in vitro Evaluation of Antitubercular Activity." Asian Journal of Chemistry 32, no. 11 (2020): 2713–21. http://dx.doi.org/10.14233/ajchem.2020.22790.

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To design and synthesize novel triazoles, indazoles and aminopyridines from various (thiophene-2-yl)prop-2-en-1-one derivatives as antitubercular leads by in silico and in vitro methods. in silco Drug design, ADME prediction and molecular docking studies were performed to assess drug likeliness and antitubercular potential of all 30 novel triazoles, indazoles and aminopyridines. in silico Drug design studies revealed that the synthetic routes applied were appropriate according to the calculations of Swiss-ADME that measure synthetic accessibility. Most of the synthesized compounds found to hav
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Zhao, Jun, Ruth Nussinov, Wen-Jin Wu, and Buyong Ma. "In Silico Methods in Antibody Design." Antibodies 7, no. 3 (2018): 22. http://dx.doi.org/10.3390/antib7030022.

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Konteatis, Zenon D. "In silico fragment-based drug design." Expert Opinion on Drug Discovery 5, no. 11 (2010): 1047–65. http://dx.doi.org/10.1517/17460441.2010.523697.

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Dahiyat, Bassil I. "In silico design for protein stabilization." Current Opinion in Biotechnology 10, no. 4 (1999): 387–90. http://dx.doi.org/10.1016/s0958-1669(99)80070-6.

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Boetker, Johan, Dhara Raijada, Johanna Aho, et al. "In silico product design of pharmaceuticals." Asian Journal of Pharmaceutical Sciences 11, no. 4 (2016): 492–99. http://dx.doi.org/10.1016/j.ajps.2016.02.010.

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Baginski, Maciej, and Katarzyna Serbakowska. "In silico design of telomerase inhibitors." Drug Discovery Today 25, no. 7 (2020): 1213–22. http://dx.doi.org/10.1016/j.drudis.2020.04.024.

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Islam, Rainul, Sumit Maji, Souparna Kabiraj, et al. "Role of in silico Drug Design in Pharmaceutical Sciences." International Journal for Research in Applied Science and Engineering Technology 10, no. 5 (2022): 2358–67. http://dx.doi.org/10.22214/ijraset.2022.42836.

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Abstract: In silico drug design is the study to identify, develop, analyze, optimize drugs or biologically cum pharmaceutically active compounds by using computerized software programs as well web servers. In silico drug design is commonly known as computer aided drug design or CADD in short. This technique shows a vital role in preclinical drug design and development. CADD can improve the speed of drug design. It reduces time as well as total cost of the experiments. Potent cum suitable molecules are prepared after performing in silico drug design including CADD. Various applications like con
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Dissertations / Theses on the topic "In silico design"

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Amengual-Rigo, Pep. "In silico design of antibodies for biomedical applications." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/672944.

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Proteins are large macromolecules constituted by amino acids that are responsible for most of the biological processes within a cell. Proteins showing high complementary affinity may bind forming protein-protein complexes. In this context, antibodies are proteins that recognize abnormal particles in the body (known as epitopes), and are elicited by means of random recombinatory events followed by strict screening selection processes. Along their production, antibodies can be modified by mutation events leading to potent antibody variants. In this sense, there is an industrial and bi
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Dörr, Alexander [Verfasser]. "In Silico Approaches for Polypharmacological Drug Design / Alexander Dörr." München : Verlag Dr. Hut, 2018. http://d-nb.info/1156510287/34.

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Jiaxi, Zhao. "In silico design of small molecular libraries via Reinforcement learning." Thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-446959.

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During the last decade, there is an increasing interest in applying deep learning in de novo drug design. In this thesis, a tool is developed to address the specific needs for generating small library for lead optimization. The optimization of small molecules is conducted given an input scaffold with defined attachment points. Various chemical fragments are proposed by the generative model and reinforcement learning is used to guide the generation to produce a library of molecules that satisfy user-defined properties. The generation is also constrained to follow user-defined reactions which ma
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Enekwa, C. Denise. "In silico design of novel binding ligands for biological targets." Thesis, Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/41067.

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An in silico design algorithm has been developed to design binding ligands for protein targets of known three-dimensional structure. In this method, the binding energy of a candidate ligand is used to ascribe it a probability of binding. A sample of a virtual library of candidate ligands is then used to ascribe implicit weights to all the ligands in the library. These weights are used to obtain virtual sub-libraries which collectively carry a greater probability to bind to the target. This algorithm is presented along with validation studies on the different algorithmic components, demonstrati
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Thovarai, Vishal. "In silico drug design of potential novel anti malarial agents /." Online version of thesis, 2009. http://hdl.handle.net/1850/8689.

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Trist, Iuni Margaret Laura. "In silico design of novel inhibitors of dengue virus replication." Thesis, Cardiff University, 2014. http://orca.cf.ac.uk/71338/.

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Dengue virus (DENV) is a health burden responsible of 50-100 million new cases and 22,000 deaths per year and its four serotypes are worryingly spreading out of the endemic regions. Current therapy is symptomatic, making antiviral research on DENV an unmet need. Vaccine development is more challenging than expected, so the development of anti-DENV drugs is particularly important for infection management. DENV is a positive sense single stranded RNA virus that replicates within cells exploiting both host and viral enzymes to replicate. Based on the hypothesis that DENV infection can be stopped
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Amrouche, Hedi. "In silico design of metal organic frameworks for greenhouse gas capture." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/in-silico-design-of-metal-organic-frameworks-for-greenhouse-gas-capture(53acdbff-69ad-43fc-94a5-2c0e632994e0).html.

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The present thesis proposes to explore the potential of Zeolitic Imidazolate Framework ZIFs for CO2 capture applications in the conditions required by the Pressure Swing Adsorption separations process. Molecular modelling methods, combining Monte Carlo, Density Functional Theory and ab-initio simulations, were employed to mimic pure and mixture gas adsorption in ZIF materials. A transferable Force Field specifically developed for ZIFs materials is used to characterize a large variety of frameworks. Theses studies enable us to better understand the phenomena acting during adsorption process. Th
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Elkaïm, Judith. "Drug design in silico : criblage virtuel de protéines à visée thérapeutique." Thesis, Bordeaux 1, 2011. http://www.theses.fr/2011BOR14444/document.

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Les processus qui mènent à la découverte de nouveaux médicaments sont longs et fastidieux, et les taux de succès sont relativement faibles. L’identification de candidats par le biais de tests expérimentaux s’avère coûteuse, et nécessite de connaître en profondeur les mécanismes d'action de la protéine visée afin de mettre en place des essais efficaces. Le criblage virtuel peut considérablement accélérer ces processus en permettant une évaluation rapide de chimiothèques de plusieurs milliers de molécules afin de déterminer lesquelles sont les plus susceptibles de se lier à une cible. Ces derniè
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Gutierrez, Rafael. "Computational Design of Nanomaterials." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-194029.

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The development of materials with tailored functionalities and with continuously shrinking linear dimensions towards (and below) the nanoscale is not only going to revolutionize state of the art fabrication technologies, but also the computational methodologies used to model the materials properties. Specifically, atomistic methodologies are becoming increasingly relevant in the field of materials science as a fundamental tool in gaining understanding on as well as for pre-designing (in silico material design) the behavior of nanoscale materials in response to external stimuli. The major lo
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Mazzolari, A. "IN SILICO APPROACHES IN DRUG DESIGN AND DEVELOPMENT: APPLICATIONS TO RATIONAL LIGAND DESIGN AND METABOLISM PREDICTION." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/347523.

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In the last decades, the applications of computational methods in medicinal chemistry have experienced significant changes which have incredibly expanded their approaches, and more importantly their objectives. The overall aim of the present research project is to explore the different fields of the modelling studies by using well-known computational methods as well as different and innovative techniques. Indeed, computational methods traditionally consisted in ligand-based and the structure-based approaches substantially aimed at optimizing the ligand structure in terms of affinity, potenc
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Books on the topic "In silico design"

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Danilo, Crippa, Rode Daniel L, and Masi Maurizio, eds. Silicon epitaxy. Academic Press, 2001.

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John, Forskitt, ed. System designs into silicon. Institute of Physics Pub., 1993.

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Lee, Manho, Jun So Pak, and Joungho Kim, eds. Electrical Design of Through Silicon Via. Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9038-3.

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Singh, Raminderpal. Silicon germanium: Technology, modeling, and design. Wiley-Interscience, 2003.

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Singh, Raminderpal. Silicon germanium: Technology, modeling, and design. IEEE Press, 2004.

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D, Cressler John, ed. Silicon heterostructure devices. CRC Press, 2008.

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D, Gajski Daniel, ed. Silicon compilation. Addison-Wesley Pub. Co., 1988.

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1948-, Baliga B. Jayant, ed. Epitaxial silicon technology. Academic Press, 1986.

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Napoli, Marzio De. Silicon carbide radiation detectors. Nova Science Publishers, 2011.

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Hahn, Gerhard. Gerhard Hahn - Kunst & Design aus Siliziumcarbid: Sieben Kooperationen 1998-2019. Wienand, 2021.

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Book chapters on the topic "In silico design"

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Dahiyat, Bassil I. "In Silico Protein Design." In Bioinformatics and Drug Discovery. Humana Press, 2006. http://dx.doi.org/10.1385/1-59259-964-8:359.

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Piplani, Sakshi, David Winkler, Yoshikazu Honda-Okubo, Varun Khanna, and Nikolai Petrovsky. "In Silico Structure-Based Vaccine Design." In Computational Vaccine Design. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3239-0_26.

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Bernardo, Paul H., and Joo Chuan Tong. "In Silico Design of Small Molecules." In Chemical Genomics and Proteomics. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-349-3_3.

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Maccari, Giuseppe, Mariagrazia Di Luca, and Riccardo Nifosì. "In Silico Design of Antimicrobial Peptides." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2285-7_9.

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Davies, Matthew N., Helene Pere, Iris Bosschem, et al. "In Silico Adjuvant Design and Validation." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6445-1_8.

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Kumar, Shailesh, and Hui Li. "In Silico Design of Anticancer Peptides." In Methods in Molecular Biology. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7201-2_17.

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Machado, Amanda Sanchez, Vivian Tamietti Martins, Maria Victoria Humbert, Myron Christodoulides, and Eduardo Antonio Ferraz Coelho. "In Silico Design of Recombinant T Peptide Epitope Vaccines for." In Vaccine Design. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1884-4_24.

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Jia, Lei, and Yaxiong Sun. "In Silico Prediction Method for Protein Asparagine Deamidation." In Computer-Aided Antibody Design. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2609-2_10.

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Villalobos, Alan, Mark Welch, and Jeremy Minshull. "In Silico Design of Functional DNA Constructs." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-564-0_15.

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Bing, Zhao, Kishore R. Sakharkar, and Meena K. Sakharkar. "In Silico Design of Epitope-based Vaccines." In Encyclopedia of Systems Biology. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_90.

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Conference papers on the topic "In silico design"

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Woicik, Addie, Zachary R. McCaw, Santiago Akle, Benjamin Dulken, Sanjana Narayanan, and Christopher Probert. "In Silico Optimization of Tissue Microarray Design for Machine Learning Analysis." In 2024 IEEE International Symposium on Biomedical Imaging (ISBI). IEEE, 2024. http://dx.doi.org/10.1109/isbi56570.2024.10635208.

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Kang, Yung Shun, Hemalatha Kilari, Neda Nazemifard, et al. "Process Design of an Industrial Crystallization Based on Degree of Agglomeration." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.193450.

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This study proposes a model-based approach utilizing a hybrid population balance model (PBM) to optimize temperature profiles for minimizing agglomeration and enhancing crystal growth. The PBM incorporates key mechanisms�nucleation, growth, dissolution, agglomeration, and deagglomeration�and is applied to the crystallization of an industrial active pharmaceutical ingredient (API), Compound K. Parameters were estimated through prior design of experiments (DoE) and refined via additional thermocycle experiments. In-silico DoE simulations demonstrate that the hybrid PBM outperforms traditional me
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Milenković, Dejan, Marko Antonijević, Edina Avdović, Dušica Simijonović, and Zoran Marković. "Design, in Silico Evaluation, and Toxicological Assessment of $N$-Protocatechoyl Hydrazone Derivatives as Potential EGFR Kinase Inhibitors." In 2024 IEEE 24th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2024. https://doi.org/10.1109/bibe63649.2024.10820446.

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Tabrizi, Seyed Zuhair Bolourchian, Elena Barbera, Wilson Ricardo Leal da Silva, and Fabrizio Bezzo. "A Python/Numpy-based package to support model discrimination and identification." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.192104.

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Addressing challenges in process design and optimisation, especially with complex models and data uncertainties, requires effective tools for model development, selection, and identification. Techniques such as Model-based Design of Experiments (MBDoE) help support this task by screening and discriminating between models and, eventually, calibrating them. Open-source and user-friendly Python packages have implemented some model identification techniques. However, the need for a tool that can couple with various model simulators and account for the steps of model identification as well as physi
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Rogers, Alexander W., Amanda Lane, Philip Martin, and Dongda Zhang. "AI-Driven Automatic Mechanistic Model Transfer Learning for Accelerating Process Development." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.167600.

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Accurate mechanistic models provide valuable physical insight and are crucial for efficient process scale-up and optimisation, but their identification requires lengthy experimental data collection, model construction, validation and discrimination. Traditional black-box machine learning transfer methods leverage prior knowledge but lack interpretability and physical insights. To address this, we propose a novel approach using artificial neural network feature attribution to automatically locate corrections and symbolic regression to make structural modifications to an inaccurate or low-fideli
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Demadis, Konstantinos D., Georgia Skordalou, and Ioannis Aristodemou. "Distinct Mechanisms of Silica Scale Formation: Silicic Acid Polycondensation and Silica Particle Growth." In CORROSION 2020. NACE International, 2020. https://doi.org/10.5006/c2020-14290.

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Abstract Silica scales are perhaps the most recalcitrant deposits in the water treatment industry. Silica scale control can be achieved either by silica removal or by chemical inhibitors. Our goal is the discovery, design and application of organic additives that have some effect on silica polycondensation. Most silica control strategies assume that silica behaves like any other mineral scale. However, silica is a profoundly different issue because of its distinctly different phisicochemical features from other scales. So, silica scale control presents a rather “unorthodox” task because the ac
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Lyu, Wenyao, and Federico Galvanin. "Automated Identification of Kinetic Models for Nucleophilic Aromatic Substitution Reaction via DoE-SINDy." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.107548.

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Nucleophilic aromatic substitutions (SNAr) are key chemical transformations in pharmaceutical and agrochemical synthesis, yet their complex mechanisms (concerted or two-step) complicate kinetic model identification. Accurate kinetic models for SNAr are essential for scale-up, optimization, and control of the reaction process, but conventional methods struggle with mechanism uncertainty driven by substrates, nucleophiles, and reaction conditions, with data collection being difficult due to its source-intensive nature. We address this using DoE-SINDy, a data-driven framework for generative model
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Huang, Hung-Jin, Fuu-Jen Tsai, Jing-Gung Chung, et al. "Drug Design for XRCC4 in Silico." In 2009 2nd International Conference on Biomedical Engineering and Informatics. IEEE, 2009. http://dx.doi.org/10.1109/bmei.2009.5304961.

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STANCIAKOVA, KATARINA, and BERT M. WECKHUYSEN. "TOWARDS IN-SILICO DESIGN OF FUNCTIONAL MATERIALS." In 25th Solvay Conference on Chemistry. WORLD SCIENTIFIC, 2021. http://dx.doi.org/10.1142/9789811228216_0011.

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Naruse, Yuki, Hiroyuki Hamada, Taizo Hanai, and Hitoshi Iba. "Evolutionary design of oscillatory genetic networks in silico." In 2015 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2015. http://dx.doi.org/10.1109/cec.2015.7257078.

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Reports on the topic "In silico design"

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Nilmeier, J., J. Fattebert, M. Jacobson, and C. Kalyanaraman. Quantum mechanical approaches to in silico enzyme characterization and drug design. Office of Scientific and Technical Information (OSTI), 2012. http://dx.doi.org/10.2172/1034511.

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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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Tangpasuthadol, Varawut, and Amarawan Intasiri. Silica reinforement of natural rubber by sol-gel process in latex. Chulalongkorn University, 2005. https://doi.org/10.58837/chula.res.2005.32.

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Beside carbon black, silica powder is the other important filler used to reinforce various colored rubber products. In order to improve the compatibility between silica particles and rubber phase, this work has focused on preparing an NR composite, reinforced by silica generated inside the NR matrix or ‘in situ’. The silica particle was formed by a sol-gel process of tetraethoxysilane (TEOS) dispersed in NR latex. The latex used was concentrated latex having 60% rubber content, and already contained water and ammonia, two ingredients needed for the sol-gel reaction. The conversion of TEOS to s
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Huang, Cihang, Yen-Fang Su, and Na Lu. Self-Healing Cementitious Composites (SHCC) with Ultrahigh Ductility for Pavement and Bridge Construction. Purdue University, 2021. http://dx.doi.org/10.5703/1288284317403.

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Cracks and their formations in concrete structures have been a common and long-lived problem, mainly due to the intrinsic brittleness of the concrete. Concrete structures, such as rigid pavement and bridge decks, are prone to deformations and deteriorations caused by shrinkage, temperature fluctuation, and traffic load, which can affect their service life. Rehabilitation of concrete structures is expensive and challenging—not only from maintenance viewpoints but also because they cannot be used for services during maintenance. It is critical to significantly improve the ductility of concrete t
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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are
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Foxe, Michael P., and Michael F. Mayer. Conceptual Silicon Beta Cell Design. Office of Scientific and Technical Information (OSTI), 2018. http://dx.doi.org/10.2172/1464271.

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Fermilab. Conceptual Design Report: Silicon Detector Facility. Office of Scientific and Technical Information (OSTI), 1993. http://dx.doi.org/10.2172/1973863.

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McGeer, Patrick C., William R. Bush, Jonathan D. Pincus, and Alvin M. Despain. Design Considerations for a Prolog Silicon Compiler. Defense Technical Information Center, 1986. http://dx.doi.org/10.21236/ada173049.

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Stredde, Herman J. D0 Silicon Upgrade: Muon Shield Conceptual Design Report. Office of Scientific and Technical Information (OSTI), 1996. http://dx.doi.org/10.2172/1033285.

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Nishino, H., W. Yang, Z. Dohnalek, V. A. Ukraintsev, and W. J. Choyke. Silicon Crystal Heating and Thermocouple Mounting Designs. Defense Technical Information Center, 1996. http://dx.doi.org/10.21236/ada310973.

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