Relevant bibliographies by topics / Fragments optimization

Contents

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

Academic literature on the topic 'Fragments optimization'

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

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Journal articles on the topic "Fragments optimization"

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Škerlová, Jana, Vlastimil Král, Milan Fábry, Juraj Sedláček, Václav Veverka, and Pavlína Řezáčová. "Optimization of the crystallizability of a single-chain antibody fragment." Acta Crystallographica Section F Structural Biology Communications 70, no. 12 (2014): 1701–6. http://dx.doi.org/10.1107/s2053230x1402247x.

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Single-chain variable antibody fragments (scFvs) are molecules with immense therapeutic and diagnostic potential. Knowledge of their three-dimensional structure is important for understanding their antigen-binding mode as well as for protein-engineering approaches such as antibody humanization. A major obstacle to the crystallization of single-chain variable antibody fragments is their relatively poor homogeneity caused by spontaneous oligomerization. A new approach to optimization of the crystallizability of single-chain variable antibody fragments is demonstrated using a representative singl
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Rathee, Manisha, and T. V. Vijay Kumar. "DNA Fragment Assembly Using Multi-Objective Genetic Algorithms." International Journal of Applied Evolutionary Computation 5, no. 3 (2014): 84–108. http://dx.doi.org/10.4018/ijaec.2014070105.

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DNA Fragment Assembly Problem (FAP) is concerned with the reconstruction of the target DNA, using the several hundreds (or thousands) of sequenced fragments, by identifying the right order and orientation of each fragment in the layout. Several algorithms have been proposed for solving FAP. Most of these have solely dwelt on the single objective of maximizing the sum of the overlaps between adjacent fragments in order to optimize the fragment layout. This paper aims to formulate this FAP as a bi-objective optimization problem, with the two objectives being the maximization of the overlap betwe
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Recht, Michael I., Vandana Sridhar, John Badger, et al. "Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening by Nanocalorimetry and X-ray Crystallography." Journal of Biomolecular Screening 19, no. 4 (2013): 497–507. http://dx.doi.org/10.1177/1087057113516493.

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Fragment-based lead discovery (FBLD) is a technique in which small, low-complexity chemical fragments of 6 to 15 heavy atoms are screened for binding to or inhibiting activity of the target. Hits are then linked and/or elaborated into tightly binding ligands, ideally yielding early lead compounds for drug discovery. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can ov
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Ulasov, A. V., Y. V. Khramtsov, T. N. Lupanova, et al. "MNT Optimization for Intracellular Delivery of Antibody Fragments." Doklady Biochemistry and Biophysics 479, no. 1 (2018): 62–65. http://dx.doi.org/10.1134/s1607672918020023.

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Seong, Jae-Dong, and Hae-Dong Kim. "Optimization of collision avoidance maneuver planning for cluster satellites in space debris explosion situation." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 232, no. 3 (2016): 407–22. http://dx.doi.org/10.1177/0954410016682270.

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In this study, the conjunction situation when a number of explosion fragments approach four cluster satellites was simulated, and an optimum avoidance maneuver plan that mitigates this risk was established. The orbits of four deputy satellites around a virtual chief satellite were defined using the Hill–Clohessy–Wiltshire equation, and NASA’s breakup model was applied to similar altitude rocket body to simulate explosions situation. The distribution of 230 explosion fragments after an explosion was simulated, and the size and direction of the Delta-V were applied to each fragment. In this situ
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Haab, Brian B., and Richard A. Mathies. "Optimization of Single-Molecule Fluorescence Burst Detection of ds-DNA: Application to Capillary Electrophoresis Separations of 100–1000 Basepair Fragments." Applied Spectroscopy 51, no. 10 (1997): 1579–84. http://dx.doi.org/10.1366/0003702971939136.

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Methods for optimizing the dye labeling, laser excitation, and data analysis for single-molecule fluorescence burst detection of ds-DNA have been developed and then validated through capillary electrophoresis (CE) separations of 100–1000 basepair (bp) DNA. Confocal microscopy is used to observe fluorescence bursts from individual DNA fragments labeled with the intercalation dye TO6 as they pass through the ∼ 2-μm-diameter focused laser beam. The dye concentration and laser power were optimized by studying fluorescence burst intensities from pBluescript DNA fragments. The optimal TO6 concentrat
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Zahra, Sana Ali, Ayesha Imran, Faiza Khalid, and Mubashir Rehman. "Fragment-Based Approach towards the Design of Potent and Versatile Anti-Cancer Agents." Global Drug Design & Development Review V, no. I (2020): 1–14. http://dx.doi.org/10.31703/gdddr.2020(v-i).01.

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Despite years of clinical research and trials of encouraging new therapies, cancer remains a leading cause of morbidity and mortality. The fragment-based drug discovery has evolved formerly as an efficient approach for identification, optimization, and generation of lead. After identifying the fragments having binding affinity with the target using computational method for fragment screening, they are optimized into more active compounds. This review elaborates the application of methodology of fragment-based drug design in designing potent and versatile anti-cancer drug candidates. It compris
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Suresh, Blessy M., Weichao Li, Peiyuan Zhang, et al. "A general fragment-based approach to identify and optimize bioactive ligands targeting RNA." Proceedings of the National Academy of Sciences 117, no. 52 (2020): 33197–203. http://dx.doi.org/10.1073/pnas.2012217117.

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RNAs have important functions that are dictated by their structure. Indeed, small molecules that interact with RNA structures can perturb function, serving as chemical probes and lead medicines. Here we describe the development of a fragment-based approach to discover and optimize bioactive small molecules targeting RNA. We extended the target validation method chemical cross-linking and isolation by pull-down (Chem-CLIP) to identify and map the binding sites of low molecular weight fragments that engage RNA or Chem-CLIP fragment mapping (Chem-CLIP-Frag-Map). Using Chem-CLIP-Frag-Map, we ident
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Zhao, Minrui, Hongni Gao, Qi Han, Jiaang Ge, Wei Wang, and Jue Qu. "Development of a Driving Cycle for Fuzhou Using K-Means and AMPSO." Journal of Advanced Transportation 2021 (February 24, 2021): 1–15. http://dx.doi.org/10.1155/2021/5430137.

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The driving cycle is a speed-to-time curve, a fundamental technique in the automotive industry, and also a basis to set standards for fuel consumption and emissions of vehicles. A driving cycle is developed based on firsthand driving data collected from fieldwork. First, bad data in the original dataset are preprocessed, the time-series standard smoothing algorithm is used to smoothen the data, and Lagrange’s interpolation is used to realize data interpolation. Next, the rules for kinematic fragment extraction are set to divide the data into kinematic fragments. Last, an evaluation system of k
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Kurniawati, Siti, and Sri Hartati. "Optimization Of The Annealing Temperature With Degenerate Primer For Amplification Of Arginine Decarboxylase (ADC) Fragment Gene From Genomic DNA of Maluku Tenggara Local Cassava." Jurnal ILMU DASAR 19, no. 2 (2018): 135. http://dx.doi.org/10.19184/jid.v19i2.6261.

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Arginine decarboxylase (ADC) is a key enzyme responsible for polyamines biosynthesis and has been shown to increase resistance to biotic and abiotic stress. Cassava (Manihot esculenta Crantz.) is able to grow and produce storage roots well on marginal land. The purpose of this study was to optimize annealing temperature of primers in PCR reaction to amplify candidate cassava ADC gene fragments. Annealing temperature is a crucial factor in PCR reaction affecting product (gene fragments) specificity. Four pairs of primers; MeADC1, MeADC2, MeADC3, andMeADC4, were designed using degenerate method
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Dissertations / Theses on the topic "Fragments optimization"

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Zahid, Muhammad. "Design and Optimization of Recombinant Antibodies Directed Against Platelet Glycoprotein VI with Therapeutic and Diagnostic Potentials." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00922980.

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Human platelets glycoprotein VI (GPVI) is evidenced to be a platelet receptor of major importance in the occurrence of arterial thrombosis. Thus, it can be considered to be of great interest in diagnosis and therapeutic of atheriosclerotic diseases. Antibodies are powerful molecules which can be used in both diagnostic as well as for therapeutic purposes due to their unique characteristics. Monoclonal and recombinant antibodies have antigen restricted specificity, high affinity and can be used in various assays. Moreover, the good knowledge of their structure and molecular engineering faciliti
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Louçano, João [Verfasser]. "Synthesis and Optimization of Group B Streptococcus Capsular Polysaccharide Fragments Using the Glyconeer / João Louçano." Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1215571879/34.

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Souza, Alfredo Danilo Ferreira de. "Otimização de novos inibidores da di-idrofolato redutase de Mycobaterium tuberculosis (mtDHFR): Docking molecular, sí­ntese, avaliação da inibição enzimática e da atividade antimicobacte." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/9/9138/tde-28012019-115311/.

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A tuberculose (TB) é considerada uma das principais doenças infecciosas e apresenta fatores críticos como a relação com o HIV/AIDS, tratamento longo e a resistência a múltiplos fármacos. A enzima di-hidrofolato redutase das micobactérias (mtDHFR) é um alvo pouco explorado e apresenta grande potencial para o desenvolvimento de novos fármacos contra TB. Estudos preliminares obtiveram fragmentos com baixa afinidade à mtDHFR, entretanto com potencial para otimização. Com isso, o fragmento foi usado como protótipo para a proposição de 22 análogos. Os compostos foram planejados utilizando informaçõe
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Rachman, Moira. "Fragment-to-Lead Optimization with Automated and Iterative Virtual Screening." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/671756.

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Fragment-based drug design is an established strategy of finding new drugs. Instead of doing mass screening of chemical libraries containing compounds that are already lead-like, starting from a small fragment can be be a more efficient strategy, because fragment space can actually represent a much larger chemical space than an equally sized library of lead-like compounds. This strategy has led to the discovery of binders for targets where high-throughput screening has previously failed. However, because fragments are small they bind with low affinity, and must be optimized into high affinity
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Khattri, Ram Bahadur. "Identifying selective ligands for glutaredoxin proteins with fragment based drug design approach and optimization of the bacterial selective hits." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1460988438.

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Ali, Rashid Majid Yousif. "Fragment-screening by X-ray crystallography of human vaccinia related kinase 1." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-166811.

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Fragment-screening by X-ray crystallography (XFS) is an expensive and low throughput fragment drug discovery screening method, and it requires a lot of optimization for each protein target. The advantages with this screening method are that it is very sensitive, it directly gives the three-dimensional structure of the protein-fragment complexes, and false positives are rarely obtained. The aim of this project was to help Sprint Bioscience assess if the advantages with XFS outweigh the disadvantages, and if this method should be used as a complement to their differential scanning fluorimetry (D
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Kulkarni, Sameer Shamrao. "Development and Optimization of Kinetic Target-Guided Synthesis Approaches Targeting Protein-Protein Interactions of the Bcl-2 Family." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4351.

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Kinetic target-guided synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting f
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Schäfer, Anja [Verfasser], and Hans Georg [Akademischer Betreuer] Bock. "An optimizational approach for an algorithmic reassembly of fragmented objects / Anja Schäfer ; Betreuer: Hans Georg Bock." Heidelberg : Universitätsbibliothek Heidelberg, 2015. http://d-nb.info/1180301536/34.

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Ferreira, Ana Raquel Santos. "A systems biology framework for pathway level culture media engineering: pplication to Pichia pastoris cultures." Doctoral thesis, Faculdade de Ciências e Tecnologia, 2012. http://hdl.handle.net/10362/9369.

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Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica<br>Culture media (CM) formulations contain hundreds of ingredients in aqueous solutions that may be involved in complex interactions in the same or competing pathways within the cell. This thesis proposes a new methodology for determining the optimal composition of CM that migrates from an empirical to a mechanistic or hybrid mechanistic CM development approach. A framework consisting in the execution of an array of cell cultures, endpoint exometabolomic assays and bioinformatics algorithm were brought together in
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Entzminger, Kevin Clifford. "Engineering antibody and T cell receptor fragments : from specificity design to optimization of stability and affinity." Thesis, 2014. http://hdl.handle.net/2152/28321.

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B and T cells comprise the two major arms of the adaptive immune response tasked with clearing and preventing infection; molecular recognition in these cells occurs through antibodies and T cell receptors (TCRs), respectively. Highly successful therapeutics, clinical diagnostics and laboratory tools have been engineered from fragments of these parent molecules. The binding specificity, affinity and biophysical characteristics of these fragments determine their potential applications and resulting efficacies. Thus engineering desired properties into antibody and TCR fragments is a major concern
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Book chapters on the topic "Fragments optimization"

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Zaporozhets, Dmitry, and Daria Zaruba. "Bacterial Foraging Optimization for VLSI Fragments Placement." In Advances in Intelligent Systems and Computing. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-68321-8_35.

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Van Herwegen, Joachim, Ruben Verborgh, Erik Mannens, and Rik Van de Walle. "Query Execution Optimization for Clients of Triple Pattern Fragments." In The Semantic Web. Latest Advances and New Domains. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-18818-8_19.

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Vaithilingam, Krishnakumar, and Sameer Mahmood Zaheer. "Optimization and Validation of Amine Coupling of Ligand." In Methods for Fragments Screening Using Surface Plasmon Resonance. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-1536-8_9.

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Vaithilingam, Krishnakumar, and Sameer Mahmood Zaheer. "Optimization and Validation of Strepavidin/Biotin-Based Capture of Ligand." In Methods for Fragments Screening Using Surface Plasmon Resonance. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-1536-8_10.

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Heling, Lars, and Maribel Acosta. "Cost- and Robustness-Based Query Optimization for Linked Data Fragments." In Lecture Notes in Computer Science. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-62419-4_14.

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Sangkavichitr, Chalermsub, and Prabhas Chongstitvatana. "Fragment as a Small Evidence of the Building Blocks Existence." In Evolutionary Learning and Optimization. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12834-9_2.

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Edink, Ewald, Gerdien E. de Kloe, and Iwan J. P. de Esch. "CHAPTER 9. Exploring Fragment Screening and Optimization Strategies Using Acetylcholine-Binding Protein." In Fragment-Based Drug Discovery. Royal Society of Chemistry, 2015. http://dx.doi.org/10.1039/9781782620938-00214.

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Alba, Enrique, and Gabriel Luque. "A New Local Search Algorithm for the DNA Fragment Assembly Problem." In Evolutionary Computation in Combinatorial Optimization. Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-71615-0_1.

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Alba, Enrique, and Gabriel Luque. "A Hybrid Genetic Algorithm for the DNA Fragment Assembly Problem." In Recent Advances in Evolutionary Computation for Combinatorial Optimization. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-70807-0_7.

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Ferenczy, György G., and György M. Keserű. "Ligand Efficiency Metrics and their Use in Fragment Optimizations." In Fragment-based Drug Discovery Lessons and Outlook. Wiley-VCH Verlag GmbH & Co. KGaA, 2016. http://dx.doi.org/10.1002/9783527683604.ch04.

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Conference papers on the topic "Fragments optimization"

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Minjuan, Zhong. "An Effective Search Results Semantic Optimization Clustering Method for XML Fragments." In 2013 International Conference on Computer Sciences and Applications (CSA). IEEE, 2013. http://dx.doi.org/10.1109/csa.2013.117.

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Abdelbaset, Reda, Yehva H. Ghallab, Yehea Ismail, and Mohamed T. El-Wakad. "Optimization of micro-electrodes for DNA fragments labelled to microbeads manipulation and characterization." In 2019 31st International Conference on Microelectronics (ICM). IEEE, 2019. http://dx.doi.org/10.1109/icm48031.2019.9021935.

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Minjuan, Zhong. "Finding Good XML Fragments Based on k-Medoid Cluster Number Optimization and Ranking Model for Feedback." In 2013 International Conference on Information Technology and Applications (ITA). IEEE, 2013. http://dx.doi.org/10.1109/ita.2013.83.

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Suwa, Tohru, Hamid Hadim, and Yong Shi. "Multidisciplinary Design and Optimization for Oscillating Flow Polymerase Chain Reaction Microfluidics Device." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11820.

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A Polymerase Chain Reaction (PCR) process is almost always required prior to DNA (deoxyribonucleic acid) analysis to create multiple copies of DNA fragments. Using microfluidics technology, the PCR process requires much shorter process time and much less DNA samples than conventional PCR systems. Among existing microfluidics-based techniques, the oscillating flow PCR has advantages including faster analysis time than cavity PCR microfluidics, and smaller contact area between the sample and polymer channel wall compared to flow-through PCR. The smaller contact area reduces DNA adsorption and en
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Panfilov, A. V., Yu M. Konstantinov, and M. V. Koulintchenko. "THE OPTIMIZATION OF CLONING OF LONG-SIZED DNA FRAGMENTS IN p-GEM VECTOR, CONTAINING TERMINAL INVERTED REPEATS OF LINEAR MITOCHONDRIAL PLASMIDS FROM ZEA MAYS." In The Second All-Russian Scientific Conference with international participation "Regulation Mechanisms of Eukariotic Cell Organelle Functions". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-318-1-84-86.

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Hagen, Alexander R., Thomas F. Grimes, Brian C. Archambault, Trevor N. Harris, and Rusi P. Taleyarkhan. "Characterization and Optimization of a Tensioned Metastable Fluid Nuclear Particle Sensor Using Laser Based Profilimetry." In 2014 22nd International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/icone22-30325.

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State of the art neutron detectors lack capabilities required by the fields of homeland security, health physics, and even for direct in-core nuclear power monitoring. A new system being developed at Purdue’s Metastable Fluid and Advanced Research Laboratory in conjunction with S/A Labs, LLC provides capabilities the state of the art lacks, and simultaneously with beta (β) and gamma (γ) blindness, high (&gt; 90% intrinsic) efficiency for neutron/alpha spectroscopy and directionality, simple detection mechanism, and lowered electronic component dependence. This system, the Tensioned Metastable
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Mallen-Fullerton, Guillermo M., and Guillermo Fernandez-Anaya. "DNA fragment assembly using optimization." In 2013 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2013. http://dx.doi.org/10.1109/cec.2013.6557749.

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Goldin, Graham, Zhuyin Ren, Yang Gao, Tianfeng Lu, Hai Wang, and Rui Xu. "HEEDS Optimized HyChem Mechanisms." In ASME Turbo Expo 2017: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/gt2017-64407.

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Transportation fuels consist of a large number of hydrocarbon components and combust through an even larger number of intermediates. Detailed chemical kinetic models of these fuels typically consist of hundreds of species, and are computationally expensive to include directly in 3D CFD simulations. HyChem (Hybrid Chemistry) is a recently proposed modeling approach for high-temperature fuel oxidation based on the assumptions that fuel pyrolysis is fast compared to the subsequent oxidation of the small fragments, and that, although their proportions may differ, all fuels pyrolyse to similar sets
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Veira, Neil, Brian Keng, Kanchana Padmanabhan, and Andreas Veneris. "Unsupervised Embedding Enhancements of Knowledge Graphs using Textual Associations." In Twenty-Eighth International Joint Conference on Artificial Intelligence {IJCAI-19}. International Joint Conferences on Artificial Intelligence Organization, 2019. http://dx.doi.org/10.24963/ijcai.2019/725.

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Knowledge graph embeddings are instrumental for representing and learning from multi-relational data, with recent embedding models showing high effectiveness for inferring new facts from existing databases. However, such precisely structured data is usually limited in quantity and in scope. Therefore, to fully optimize the embeddings it is important to also consider more widely available sources of information such as text. This paper describes an unsupervised approach to incorporate textual information by augmenting entity embeddings with embeddings of associated words. The approach does not
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Chakraborty, Soham, and Viktor Vafeiadis. "Formalizing the concurrency semantics of an LLVM fragment." In 2017 IEEE/ACM International Symposium on Code Generation and Optimization (CGO). IEEE, 2017. http://dx.doi.org/10.1109/cgo.2017.7863732.

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Reports on the topic "Fragments optimization"

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Chen, J. S. J. Distributed-query optimization in fragmented data-base systems. Office of Scientific and Technical Information (OSTI), 1987. http://dx.doi.org/10.2172/7183881.

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DeRonne, Kevin W., and George Karypis. Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction. Defense Technical Information Center, 2006. http://dx.doi.org/10.21236/ada444732.

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