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Journal articles on the topic 'Design à base de fragments'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Nair, Pramod C., Alpeshkumar K. Malde, Nyssa Drinkwater, and Alan E. Mark. "Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design." ACS Medicinal Chemistry Letters 3, no. 4 (2012): 322–26. http://dx.doi.org/10.1021/ml300015u.

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Zhang, Sixue, Atefeh Garzan, Nicole Haese, et al. "Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design." PLOS ONE 16, no. 1 (2021): e0245013. http://dx.doi.org/10.1371/journal.pone.0245013.

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The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5

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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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Pidnebesna, Halyna A. "The Design of Inductive Modeling Tools Using Ontologies." Control Systems and Computers, no. 6 (290) (December 2020): 46–54. http://dx.doi.org/10.15407/csc.2020.06.046.

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The architecture of the GMDH-based inductive modeling tools is considered. A feature is the use of the knowledge base in the form of an ontology of the subject area of inductive modeling. The application of the ontological approach to the design of the knowledge base makes it possible to automatically acquire new knowledge, efficiently process information in the modeling of complex objects of different nature according to statistical data, generate queries and obtain logical inferences. Fragments of the GMDH-based inductive modeling ontology are given as an example of creating a formal descrip

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Li, Yong, Dong Chen, Ming Jiang, and Zonghao Tian. "Research on the Characteristic of Projectile Fragments Dispersion Based on Fragment Warhead Design." IOP Conference Series: Materials Science and Engineering 573 (August 2, 2019): 012104. http://dx.doi.org/10.1088/1757-899x/573/1/012104.

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Padilha, Ricardo, Jose Luiz Portugal, Adriano Vicente dos Santos, Sônia Valeria Pereira, and Tiago Vinícius Batista do Carmo. "Proposição de Modelo de Corredores Ecológicos com Base no Sistema de Informações Geográficas na Região de Suape, Pernambuco, Brasil (Propose a Model for Ecological Corridors Based on Geographic Information System in the Region of Suape, Pernambuco,...)." Revista Brasileira de Geografia Física 9, no. 1 (2016): 079. http://dx.doi.org/10.26848/rbgf.v9.1.p079-090.

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A expansão de áreas agrícolas e urbanas, a implementação de projetos industriais, entre outras atividades antrópicas, promovem a alteração da paisagem original, criando outra, dominada por vários remanescentes da vegetação nativa. Estes remanescentes, denominados também de fragmentos florestais, são fundamentais para manutenção da biodiversidade existente no local. Porém uma paisagem fragmentada torna os remanescentes florestais isolados vulneráveis, nesse sentido, torna-se importante a concepção de conexões para interligar os fragmentos, diminuindo a pressão sobre sua diversidade e aumentando

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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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8

Lee, Hyukzae, Jonghee Kim, Chanho Jung, Yongchan Park, Woong Park, and Jihong Son. "A Deep Learning-Based Fragment Detection Approach for the Arena Fragmentation Test." Applied Sciences 10, no. 14 (2020): 4744. http://dx.doi.org/10.3390/app10144744.

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The arena fragmentation test (AFT) is one of the tests used to design an effective warhead. Conventionally, complex and expensive measuring equipment is used for testing a warhead and measuring important factors such as the size, velocity, and the spatial distribution of fragments where the fragments penetrate steel target plates. In this paper, instead of using specific sensors and equipment, we proposed the use of a deep learning-based object detection algorithm to detect fragments in the AFT. To this end, we acquired many high-speed videos and built an AFT image dataset with bounding boxes

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Aguirre, Clémentine, Tim ten Brink, Jean-François Guichou, Olivier Cala, and Isabelle Krimm. "Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5." PLoS ONE 9, no. 7 (2014): e102300. http://dx.doi.org/10.1371/journal.pone.0102300.

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Hidayat, Muhammad Fauzi, Eka Gunarti Ningsih, Ahmad Husein Alkaff та Usman Sumo Friend Tambunan. "Discovery of Novel α-Amylase Inhibitors as Type Two Diabetes Mellitus Therapy through Fragment-Based Drug Design". Key Engineering Materials 840 (квітень 2020): 237–44. http://dx.doi.org/10.4028/www.scientific.net/kem.840.237.

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Diabetes is one of the top causes of death in the world, with 425 million sufferers reported in 2017. About 90% of diabetics suffer from Type 2 Diabetes Mellitus (T2DM). Recent studies show that inhibiting the α-amylase enzyme can significantly decrease the postprandial blood glucose levels through blocking carbohydrate hydrolysis. Therefore, it can be a promising strategy for T2DM treatment. This research was aimed to find the new potential inhibitor for the α-amylase from lead-like compounds Molecular Operating Environment (MOE) database through fragment-based drug design, combining with str

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Koh, Cho Yeow, Latha Kallur Siddaramaiah, Ranae M. Ranade, et al. "A binding hotspot inTrypanosoma cruzihistidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens." Acta Crystallographica Section D Biological Crystallography 71, no. 8 (2015): 1684–98. http://dx.doi.org/10.1107/s1399004715007683.

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American trypanosomiasis, commonly known as Chagas disease, is a neglected tropical disease caused by the protozoan parasiteTrypanosoma cruzi. The chronic form of the infection often causes debilitating morbidity and mortality. However, the current treatment for the disease is typically inadequate owing to drug toxicity and poor efficacy, necessitating a continual effort to discover and develop new antiparasitic therapeutic agents. The structure ofT. cruzihistidyl-tRNA synthetase (HisRS), a validated drug target, has previously been reported. Based on this structure and those of human cytosoli

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Park, In, Jae-Hoo Lee, Hwan-Sub Hyun, Min-Joon Oh, and Sang-Jin Shin. "Effects of Bone Incorporation After Arthroscopic Stabilization Surgery for Bony Bankart Lesion Based on Preoperative Glenoid Defect Size." American Journal of Sports Medicine 46, no. 9 (2018): 2177–84. http://dx.doi.org/10.1177/0363546518773317.

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Background: Recurrent shoulder instability occurs more frequently after soft tissue surgery when the glenoid defect is greater than 20%. However, for lesions less than 20%, no scientific guidance is available regarding what size of bone fragments may affect shoulder functional restoration after bone incorporation. Purpose/Hypothesis: The purpose was to analyze how preoperative glenoid defect size and bone fragment incorporation alter postoperative clinical outcomes, we compared the functional outcomes of shoulders with and without bony Bankart lesion. It was hypothesized that differences in po

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Singh, Arjan, Karanjeet Singh Kahlon, and Rajinder Singh Virk. "Nonreplicated Static Data Allocation in Distributed Databases Using Biogeography-Based Optimization." Chinese Journal of Engineering 2014 (February 23, 2014): 1–9. http://dx.doi.org/10.1155/2014/785321.

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Allocation of data is one of the key design issues of distributed database. A major cost of query execution in a distributed database system is the data transfer cost from one site to another site. The allocation of fragments among the different sites over the network plays an important role in performance of the distributed database system. The main objective of a data allocation in distributed database is to place the data fragments at different sites in such a way, so that the total data transfer cost can be minimized while executing a set of queries. In this paper, a new biogeography-based

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Plais, Romain, Hamza Boufroura, Guy Gouarin, et al. "Design and property investigation on a five-interaction-based fluorescent anion receptor clip." RSC Advances 11, no. 16 (2021): 9476–87. http://dx.doi.org/10.1039/d1ra00630d.

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15

Hajduk, Philip J., Arthur Gomtsyan, Stanley Didomenico, et al. "Design of Adenosine Kinase Inhibitors from the NMR-Based Screening of Fragments." Journal of Medicinal Chemistry 43, no. 25 (2000): 4781–86. http://dx.doi.org/10.1021/jm000373a.

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16

Abitbol, Roy, Ilan Shimshoni, and Jonathan Ben-Dov. "Machine Learning Based Assembly of Fragments of Ancient Papyrus." Journal on Computing and Cultural Heritage 14, no. 3 (2021): 1–21. http://dx.doi.org/10.1145/3460961.

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The task of assembling fragments in a puzzle-like manner into a composite picture plays a significant role in the field of archaeology as it supports researchers in their attempt to reconstruct historic artifacts. In this article, we propose a method for matching and assembling pairs of ancient papyrus fragments containing mostly unknown scriptures. Papyrus paper is manufactured from papyrus plants and therefore portrays typical thread patterns resulting from the plant’s stems. The proposed algorithm is founded on the hypothesis that these thread patterns contain unique local attributes such t

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Kozakiewicz, Marcin, Rafal Zieliński, Michał Krasowski, and Jakub Okulski. "Forces Causing One-Millimeter Displacement of Bone Fragments of Condylar Base Fractures of the Mandible after Fixation by All Available Plate Designs." Materials 12, no. 19 (2019): 3122. http://dx.doi.org/10.3390/ma12193122.

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Background: There has been no direct comparison of all existing plates dedicated for fracture osteosynthesis of mandibular condyle base until now. The aim of the study was to test mechanically all available designs of titanium plates on the market on polyurethane mandibles using an individually designed clamping system. Methods: Forces required for a 1 mm displacement of fixed fracture and incidents of screw loosening were recorded. Results indicated the best mechanical plates among all existing designs available. Results: It has occured that some of osseofixation plates should not be used any

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Garner, Philip, Philip B. Cox, Upendra Rathnayake, Nicholas Holloran, and Paul Erdman. "Design and Synthesis of Pyrrolidine-based Fragments That Sample Three-dimensional Molecular Space." ACS Medicinal Chemistry Letters 10, no. 5 (2019): 811–15. http://dx.doi.org/10.1021/acsmedchemlett.9b00070.

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19

Eriksson, Susann, Markus Vehniäinen, Tove Jansén, et al. "Dual-Label Time-resolved Immunofluorometric Assay of Free and Total Prostate-specific Antigen Based on Recombinant Fab Fragments." Clinical Chemistry 46, no. 5 (2000): 658–66. http://dx.doi.org/10.1093/clinchem/46.5.658.

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Abstract Background: Recombinant Fab fragments are attractive as reagents for novel sandwich immunoassays, but no such assays have been described. We developed a dual-label two-site immunoassay based entirely on recombinant Fab fragments and compared it to the same assay with intact monoclonal antibodies. Methods: The capture Fab fragment, which binds free prostate-specific antigen (PSA) and PSA in complex with α1-antichymotrypsin on an equimolar basis, is site-specifically biotinylated and attached to the solid phase in streptavidin-coated microtitration wells. The Fab fragment that detects o

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Dörgő, Gyula, and János Abonyi. "Group Contribution Method-based Multi-objective Evolutionary Molecular Design." Hungarian Journal of Industry and Chemistry 44, no. 1 (2016): 39–50. http://dx.doi.org/10.1515/hjic-2016-0005.

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Abstract The search for compounds exhibiting desired physical and chemical properties is an essential, yet complex problem in the chemical, petrochemical, and pharmaceutical industries. During the formulation of this optimization-based design problem two tasks must be taken into consideration: the automated generation of feasible molecular structures and the estimation of macroscopic properties based on the resultant structures. For this structural characteristic-based property prediction task numerous methods are available. However, the inverse problem, the design of a chemical compound exhib

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21

Sepay, Nayim, Pranab Chandra Saha, Zarrin Shahzadi, Aratrika Chakraborty, and Umesh Chandra Halder. "A crystallography-based investigation of weak interactions for drug design against COVID-19." Physical Chemistry Chemical Physics 23, no. 12 (2021): 7261–70. http://dx.doi.org/10.1039/d0cp05714b.

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Via analyzing 143 crystal structures of SARS-CoV-2 M<sup>pro</sup>, we identified the most important active site amino acids, the nature and propensity of their interactions with small molecules and the relevant fragments of ligands to design new pharmacophores.

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22

Sewisy, Adel A., Ali A. Amer, and Hassan I. Abdalla. "A Novel Query-Driven Clustering-Based Technique for Vertical Fragmentation and Allocation in Distributed Database Systems." International Journal on Semantic Web and Information Systems 13, no. 2 (2017): 27–54. http://dx.doi.org/10.4018/ijswis.2017040103.

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In this paper, heuristic query-driven clustering-based vertical fragmentation technique is efficiently developed. The intrinsic idea is to meet the idealistic case of DDBS design which comes to happen as each query attune “closely match” its relevant fragment. The proposed technique is mainly sought to breed clusters of queries in the first place. Consequently, these clusters would be tacitly used to generate intended disjoint fragments. Moreover, the allocation process has been considered so that replicated and non-replicated scenarios of data are applied. This technique basically meant to be

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Megnassan, Eugene, Issouf Fofana, Brice Dali, Frederica Mansilla Koblavi, Vladimir Frecer, and Stanislav Miertus. "Structure-Based Design of Tetrahydroisoquinoline-Based Hydroxamic Acid Derivatives Inhibiting Human Histone Deacetylase 8." SDRP Journal of Computational Chemistry & Molecular Modeling 5, no. 1 (2021): 504–38. http://dx.doi.org/10.25177/jccmm.5.1.ra.10708.

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We have designed new human histone deacetylase 8 (HDAC8) inhibitors using structure-based molecular design. 3D models of HDAC8–inhibitor complexes were prepared by in situ modification of the crystal structure of HDAC8 co-crystallized with the hydroxamic acid suberoylanilide (SAHA) and a training set (TS) of tetrahydroisoquinoline-based hydroxamic acid derivatives (DAHTs) with known inhibitory potencies. A QSAR model was elaborated for the TS yielding a linear correlation between the computed Gibbs free energies (GFE) of HDAC8–DAHTs complexation (∆∆Gcom) and observed half-maximal enzyme inhibi

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Iosifov, P. A., and A. S. Pervanyuk. "Application of web-oriented approach based on information fragments in design of training tools." Automation and Remote Control 74, no. 12 (2013): 2106–11. http://dx.doi.org/10.1134/s0005117913120114.

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Schloss, Patrick D., Matthew L. Jenior, Charles C. Koumpouras, Sarah L. Westcott, and Sarah K. Highlander. "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system." PeerJ 4 (March 28, 2016): e1869. http://dx.doi.org/10.7717/peerj.1869.

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Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina’s MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the

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Neff, Andreas, Carl-Peter Cornelius, Michael Rasse, DanielDalla Torre, and Laurent Audigé. "The Comprehensive AOCMF Classification System: Condylar Process Fractures - Level 3 Tutorial." Craniomaxillofacial Trauma & Reconstruction 7, no. 1_suppl (2014): 44–58. http://dx.doi.org/10.1055/s-0034-1389559.

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This tutorial outlines the detailed system for fractures of the condylar process at the precision level 3 and is organized in a sequence of sections dealing with the description of the classification system within topographical subdivisions along with rules for fracture coding and a series of case examples with clinical imaging. Basically, the condylar process comprises three fracture levels and is subdivided into the head region, the condylar neck, and the condylar base. Fractures of the condylar head show typical fracture lines either within the lateral pole zone, which may lead to loss of v

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Prasad, V. Vara. "Design and Analysis of Vehicle Mine Blast Using AUTODYN." International Journal for Research in Applied Science and Engineering Technology 9, no. VII (2021): 1929–35. http://dx.doi.org/10.22214/ijraset.2021.36750.

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Anti-vehicular (AV) mines are capable of disabling a heavy vehicle, or completely destroying a lighter vehicle. The most common form of AV mine is the blast mine, which uses a large amount of explosive to directly damage the target. In a conventional military setting, landmines are used as a defensive force-multiplier and to restrict the movements of the opposing force. They are relatively cheap to purchase and easy to acquire, hence landmines are also potent weapons in the insurgents’ armamentarium. The stand-off nature of its design has allowed insurgents to cause significant injuries to sec

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Smets, T., J. Poesen, and E. Bochet. "Impact of plot length on the effectiveness of different soil-surface covers in reducing runoff and soil loss by water." Progress in Physical Geography: Earth and Environment 32, no. 6 (2008): 654–77. http://dx.doi.org/10.1177/0309133308101473.

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Covering the soil surface by rock fragments, organic mulches or vegetation is often done to reduce runoff and soil loss by water erosion compared to a bare soil treatment. The runoff or erosion-reducing effectiveness of these soil surface covers has been investigated for a range of plot lengths under different environmental conditions. Recent research indicates that the effectiveness of soil surface covers in reducing runoff and soil loss by water erosion may be affected by the size of the laboratory or field plots (ie, spatial scale). Therefore, the main objective of this review is to explore

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Alkaff, Ahmad Husein, Mutiara Saragih, Shabrina Noor Imana, Mochammad Arfin Fardiansyah Nasution, and Usman Sumo Friend Tambunan. "Identification of DNA Methyltransferase-1 Inhibitor for Breast Cancer Therapy through Computational Fragment-Based Drug Design." Molecules 26, no. 2 (2021): 375. http://dx.doi.org/10.3390/molecules26020375.

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Epimutation by DNA Methyltransferase 1 (DNMT1), an epigenetic regulator enzyme, may lead to the proliferation of breast cancer. In this report, 168,686 natural products from the PubChem database were screened and modified by in silico method to acquire the potential inhibitor of DNMT1. The initial screening of PubChem natural products using Lipinski’s and Veber’s rules of three and toxic properties have resulted in 2601 fragment candidates. Four fragments from pharmacophore-based molecular docking simulation were modified by utilizing FragFP and the Lipinski’s and Veber’s rules of five, and re

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Pukharenko, Yury, and Yury Tikhonov. "Influence of High-Porous Filling Materials and Mineral Fiber on Thermal and Fire Resistant Properties of Aerated Composites." Applied Mechanics and Materials 725-726 (January 2015): 572–77. http://dx.doi.org/10.4028/www.scientific.net/amm.725-726.572.

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Compounds were developed and properties studied of the composites on gypsum binding agent and light filling materials, exfoliated vermiculate and perlite providing high fire resistance to mortars on their base. The conducted selection of compounds with the use of a number of non-flammable fiber additives (fiberglass, chrysotile asbestos fiber) showed that the compounds with fiberglass additives had the biggest design quality ratio. The degree of influence of high-speed mortar mixture mixing on its properties was determined. Mixing speed increase up to 600 rpm allowed increasing of the design q

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Orysenko, O. V., O. G. Fenko, М. L. Zotsenko, Yu L. Vynnykov, and М. O. Kharchenko. "SUPPORTED CONSTRUCTION FOR QUARRY EXCAVATOR TRAVERS." ACADEMIC JOURNAL Series: Industrial Machine Building, Civil Engineering 1, no. 50 (2018): 46–55. http://dx.doi.org/10.26906/znp.2018.50.1058.

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It has been established that repair of quarry excavators should be carried out directly on site. In this case, the use of jacks for weighing the rotary platform of excavators Bucyrus RH340 and Terex RH200 models for repair of running equipment is impossible because of their design features. This type of repair is suggested to be performed as an excavator based on the design developed by the authors. The installation of the excavator on the support structure is carried out by its working equipment. The supporting structure is suggested to be made in the form of two identical fragments for its u

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Cerreta, Maria, Chiara Mazzarella, Martina Spiezia, and Maria Rosaria Tramontano. "Regenerativescapes: Incremental Evaluation for the Regeneration of Unresolved Territories in East Naples." Sustainability 12, no. 17 (2020): 6975. http://dx.doi.org/10.3390/su12176975.

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The unresolved territories are privileged places for the proliferation of degradation phenomena that affect the environment and human well-being. The impacts of their critical conditions go beyond the limits of the damaged urban fragments, involving the built environment, society, economy, culture, and conditioning quality of life. This paper proposes a methodological approach to landscape design supported by an evaluation framework to orient strategic design planning with specific attention to unresolved territories consistent with the circular economy perspective. The circular city principle

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Marinelli, A., S. A. Papanicolopulos, S. Kourkoulis, and I. Vayas. "The Pull-Out Problem in Restoring Marble Fragments: A Design Criterion Based on Experimental Results." Strain 45, no. 5 (2009): 433–44. http://dx.doi.org/10.1111/j.1475-1305.2008.00519.x.

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Kabir, Md Mahbubul, Denis Faure, Jacqueline Haurat, et al. "Oligonucleotide probes based on 16S rRNA sequences for the identification of four Azospirillum species." Canadian Journal of Microbiology 41, no. 12 (1995): 1081–87. http://dx.doi.org/10.1139/m95-151.

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Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few

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Araya, Kaori, Seiji Fukumoto, Rebecca Backenroth, et al. "A Novel Mutation in Fibroblast Growth Factor 23 Gene as a Cause of Tumoral Calcinosis." Journal of Clinical Endocrinology & Metabolism 90, no. 10 (2005): 5523–27. http://dx.doi.org/10.1210/jc.2005-0301.

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Context: Tumoral calcinosis is a disease characterized by ectopic calcification and hyperphosphatemia due to enhanced renal tubular phosphate reabsorption. Fibroblast growth factor (FGF)23 was identified as a responsible factor in hypophosphatemic diseases caused by renal phosphate leak. Objective: The objective of the study was to analyze the involvement of FGF23 in the development of tumoral calcinosis. Design: Serum FGF23 level was evaluated in a patient with tumoral calcinosis by two kinds of ELISA: full-length assay that detects only full-length FGF23 with phosphate-lowering activity and

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Syamsidi, Armini, Nuur Aanisah, Reyhan Fiqram, and Imanuel Al Jultri. "Primer Design and Analysis for Detection of mecA gene." Journal of Tropical Pharmacy and Chemistry 5, no. 3 (2021): 245–53. http://dx.doi.org/10.25026/jtpc.v5i3.297.

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MecA is a gene that causes antibiotic resistance and it contained in Staphylococcus aureus. The gene can be detected using pairs of primer (forward and reverse). Primes is short nucleotide that are used as attachment point for DNA polymerase and as a barrier for the fragment DNA target to be amplified with Polymerase Chain Reaction (PCR). The aims of this study were to design and analysis the nucleotide primer sequences of MecA. This research using in silico method of NCBI (National Center of Biotechnology Information) application, clone manager10, oligoanalyzer3.1, perlprimer and primer3plus.

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Chimenti, Michael S., Stacie L. Bulfer, R. Jeffrey Neitz, et al. "A Fragment-Based Ligand Screen Against Part of a Large Protein Machine." Journal of Biomolecular Screening 20, no. 6 (2015): 788–800. http://dx.doi.org/10.1177/1087057115570550.

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The ubiquitous AAA+ ATPase p97 functions as a dynamic molecular machine driving several cellular processes. It is essential in regulating protein homeostasis, and it represents a potential drug target for cancer, particularly when there is a greater reliance on the endoplasmic reticulum–associated protein degradation pathway and ubiquitin–proteasome pathway to degrade an overabundance of secreted proteins. Here, we report a case study for using fragment-based ligand design approaches against this large and dynamic hexamer, which has multiple potential binding sites for small molecules. A scree

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Tarnavchyk, Ihor, Andriy Voronov, Volodymyr Donchak, et al. "Synthesis and Selfassambling of Amphiphilic Oligoesters Based on Pyromellitic Acid." Chemistry & Chemical Technology 10, no. 2 (2016): 159–72. http://dx.doi.org/10.23939/chcht10.02.159.

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The method for synthesis of a new class of amphiphilic oligoesters of pyromellitic acid is developed. As hydrophilic fragments polyethylene glycols or polyethylene glycol mono methyl ethers were used, as lipophilic ones – primary fatty alcohols or cholesterol. The structure of the synthesized oligoesters was confirmed by IR- and PMR-spectroscopy. The oligoesters could solubilize water-insoluble substances, for example such effective antitumor lipophilic drug as curcumin. The high solubilization capacity of the OEPA assemblies and their biodegradability, as well as other properties (size distri

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Kumar, Deepak, Jyoti Batra, Claire Komives, and Anurag Rathore. "QbD Based Media Development for the Production of Fab Fragments in E. coli." Bioengineering 6, no. 2 (2019): 29. http://dx.doi.org/10.3390/bioengineering6020029.

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Ranibizumab is a biotherapeutic Fab fragment used for the treatment of age-related macular degeneration and macular oedema. It is currently expressed in the gram-negative bacterium, Escherichia coli. However, low expression levels result in a high manufacturing cost. The protein expression can be increased by manipulating nutritional requirements (carbon source, nitrogen source, buffering agent), process parameters (pH, inducer concentration, agitation, temperature), and the genetic make-up of the producing strain. Further, understanding the impact of these factors on product quality is a requ

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Winter, Anja, Alicia P. Higueruelo, May Marsh, Anna Sigurdardottir, Will R. Pitt, and Tom L. Blundell. "Biophysical and computational fragment-based approaches to targeting protein–protein interactions: applications in structure-guided drug discovery." Quarterly Reviews of Biophysics 45, no. 4 (2012): 383–426. http://dx.doi.org/10.1017/s0033583512000108.

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AbstractDrug discovery has classically targeted the active sites of enzymes or ligand-binding sites of receptors and ion channels. In an attempt to improve selectivity of drug candidates, modulation of protein–protein interfaces (PPIs) of multiprotein complexes that mediate conformation or colocation of components of cell-regulatory pathways has become a focus of interest. However, PPIs in multiprotein systems continue to pose significant challenges, as they are generally large, flat and poor in distinguishing features, making the design of small molecule antagonists a difficult task. Neverthe

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Magalhães, Joana, Nina Franko, Giannamaria Annunziato, et al. "Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand–based drug design." Journal of Enzyme Inhibition and Medicinal Chemistry 33, no. 1 (2018): 1444–52. http://dx.doi.org/10.1080/14756366.2018.1512596.

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Jain, Swati, Cigdem Bayrak, Louis Petingi, and Tamar Schlick. "Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs." Genes 9, no. 8 (2018): 371. http://dx.doi.org/10.3390/genes9080371.

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RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply

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Dörgő, Gyula, and János Abonyi. "Hierarchical Representation Based Constrained Multi-objective Evolutionary Optimisation of Molecular Structures." Periodica Polytechnica Chemical Engineering 63, no. 1 (2018): 210–25. http://dx.doi.org/10.3311/ppch.12021.

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We propose an efficient algorithm to generate Pareto optimal set of reliable molecular structures represented by group contribution methods. To effectively handle structural constraints we introduce goal oriented genetic operators to the multi-objective Non-dominated Sorting Genetic Algorithm-II (NSGA-II). The constraints are defined based on the hierarchical categorisation of the molecular fragments. The efficiency of the approach is tested on several benchmark problems. The proposed approach is highly efficient to solve the molecular design problems, as proven by the presented benchmark and

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Stepanova, L. A., M. V. Sergeeva, M. A. Shuklina, et al. "A Fusion Protein Based on the Second Subunit of Hemagglutinin of Influenza A/H2N2 Viruses Provides Cross Immunity." Acta Naturae 8, no. 2 (2016): 116–26. http://dx.doi.org/10.32607/20758251-2016-8-2-116-126.

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Conserved fragments of the second subunit of hemagglutinin (HA2) are of great interest for the design of vaccine constructs that can provide protective immunity against influenza A viruses of different subtypes. A recombinant fusion protein, FlgMH, was constructed on the basis of flagellin and a highly conserved HA2 fragment (35-107) of influenza viruses of the subtype A/H2N2, containing B cell, CD4+ T cell, and CD8+ T cell epitopes. The native conformation of the HA2 fragment was partially preserved upon its attachment to the C-terminus of flagellin within the recombinant fusion protein FlgMH

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S., Jagannatha, T. V. Suresh Kumar, and K. Rajanikanth. "Query Based Resource Allocation and Performance Prediction in Distributed Database." Journal of Communications Technology, Electronics and Computer Science 4 (February 16, 2016): 16. http://dx.doi.org/10.22385/jctecs.v4i0.43.

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Resource allocation is one of the main issues for providing services in an efficient way on distributed database. Improving the performance is one of the key research issues by proper design of efficient distributed database and proper usage of resources in information technology. The cost of each computational service depends on the amount of computations. The system resources have to be allocated in order to handle the workload and minimize the cost of computing by using proper allocation strategy. Performance is strongly related to the allocation of resources and data fragments in distribut

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Sergeev, A. V., and V. V. Sergeev. "Method of lossless compression of synthetic digital images based on selection of similar fragments." Pattern Recognition and Image Analysis 18, no. 4 (2008): 687–89. http://dx.doi.org/10.1134/s105466180804024x.

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Mau, Margit, and Kenneth N. Timmis. "Use of Subtractive Hybridization To Design Habitat-Based Oligonucleotide Probes for Investigation of Natural Bacterial Communities." Applied and Environmental Microbiology 64, no. 1 (1998): 185–91. http://dx.doi.org/10.1128/aem.64.1.185-191.1998.

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ABSTRACT We describe a rapid oligonucleotide probe design strategy based on subtractive hybridization which yields probes for 16S rRNA or rRNA genes of individual members of microbial communities that are specific within the context of those communities. This strategy circumvents the need to sequence many similar or identical clones of dominant members of a community. Radioactively labeled subfragments of a cloned 16S rRNA gene sequence for which a probe is required (target) were hybridized with biotinylated total 16S ribosomal DNA (rDNA) amplified from the microbial community, and the hybrids

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Tassinari, Martina, Alberto Lena, Elena Butovskaya, et al. "A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety." Molecules 23, no. 8 (2018): 1874. http://dx.doi.org/10.3390/molecules23081874.

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G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed

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Vulpetti, Anna, Ulrich Hommel, Gregory Landrum, Richard Lewis, and Claudio Dalvit. "Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine." Journal of the American Chemical Society 131, no. 36 (2009): 12949–59. http://dx.doi.org/10.1021/ja905207t.

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Pucci, Daniela, Anna Bellusci, Sergio Bernardini, et al. "Bioactive fragments synergically involved in the design of new generation Pt(ii) and Pd(ii)-based anticancer compounds." Dalton Transactions, no. 43 (2008): 5897. http://dx.doi.org/10.1039/b808093c.

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