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Academic literature on the topic 'KNApSAck database'

Author: Grafiati

Published: 5 June 2025

Last updated: 16 July 2025

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Journal articles on the topic "KNApSAck database"

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Abdullah, Azian Azamimi, Md Altaf-Ul-Amin, Naoaki Ono, et al. "Development and Mining of a Volatile Organic Compound Database." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/139254.

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Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases. Information on VOCs is scattered in the literature until now; however, there is still no available database describing VOCs and their biological activities. To attain this purpose, we have developed KNApSAcK Metabolite Ecology Database, which contains the information on the relationships between VOCs and their emitting organisms. The KNApSAcK Metabolite Ecology is also linked with the KNApSAcK Core and KNApSAcK Metabolite Activity Database to provide further information on the metabolites and their biological activities. The VOC database can be accessed online.

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Shinbo, Yoko, Shun-ichi Sakaguchi, Yukiko Nakamura, et al. "[Special Issue: Fact Databases and Freewares] Species-metabolite Database (KNApSAcK): Elucidating Diversity of Flavonoids." Journal of Computer Aided Chemistry 7 (2006): 94–101. http://dx.doi.org/10.2751/jcac.7.94.

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3

Rahmansyah, Rahmad. "Penerapan Algoritma Friefalds Untuk Pembangkit Kunci Algoritma Knapsack Pada Pengamanan Record Database." KLIK: Kajian Ilmiah Informatika dan Komputer 2, no. 4 (2022): 132–37. http://dx.doi.org/10.30865/klik.v2i4.317.

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Algoritma Friefalds mempunyai dua kunci, yaitu kunci publik dan kunci rahasia. Algoritma ini memiliki keamanan yang terletak pada kesulitan dalam menghitung alogaritma diskrit. Baik kunci enkripsi maupun dekripsi keduanya merupakan bilangan prima. Algoritma friefalds tipe algoritma kriptografi asimetris terdiri atas dua buah kunci yaitu kunci publick untuk melakukan enkripsi sedangkan kunci pribadi untuk melakukan dekripsi. Dalam algoritma Friefalds, kunci yang didistribusikan adalah kunci publik yang tidak diperlukan kerahasiannya sedangkan kunci pribadi tetap disimpan atau tidak didistribusikan. Setiap orang yang memiliki kunci public dapat melakukan proses implementasi enkripsi tetapi hasil dari enkripsi tersebut hanya bias dibaca oleh orang yang memiliki kunci pribadi. Untuk meningkatkan kekuatan dari algoritma tersebut, maka kunci yang digunakan untuk melakukan proses enkripsi dan dekripsi akan dimodifikasi terlebih dahulu menggunakan algoritma pengacakan yaitu Algoritma Knapsack. Algoritma Knapsack adalah algoritma acak probabilistik yang digunakan untuk memverifikasi perkalian matriks. Tujuan dalam menggunakan algoritma Freifalds ini adalah agar kunci yang dihasilkan lebih sulit ditebak sehingga mempersulit kriptanalis dalam membaca pesan atau informasi tersebut.

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Nakamura, Kensuke, Naoki Shimura, Yuuki Otabe, et al. "KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites." Plant and Cell Physiology 54, no. 2 (2013): e4-e4. http://dx.doi.org/10.1093/pcp/pcs186.

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Lianza, Mariacaterina, Ritchy Leroy, Carine Machado Rodrigues, et al. "The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case." Molecules 26, no. 3 (2021): 637. http://dx.doi.org/10.3390/molecules26030637.

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The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from Urceolina peruviana, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.

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Nakamura, Y., F. Mochamad Afendi, A. Kawsar Parvin, et al. "KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities." Plant and Cell Physiology 55, no. 1 (2013): e7-e7. http://dx.doi.org/10.1093/pcp/pct176.

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Prabasari, Kartika, Nia Kurnianingsih, and Nia Kurniawan. "In silico Exploration of Bioactive Compounds from Withania somnifera as Inhibitor for Alpha Delta Bungarotoxin of Bungarus candidus Venom." Biotropika: Journal of Tropical Biology 11, no. 2 (2023): 64–73. http://dx.doi.org/10.21776/ub.biotropika.2023.011.02.01.

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The antivenom for Malayan krait (Bungarus candidus) venom has not yet been available in Indonesia, leading to many fatal snakebite cases. Alternative treatment approaches using medicinal plants are needed to be explored. This study investigated the potential of medicinal plants natural bioactive compounds as toxic alpha-delta protein bungarotoxin inhibitor in B. candidus venom. The approach taken is using the 3D structure of the alpha-delta protein of bungarotoxin B. candidus predicted by SWISS-MODEL. Knapsack Family Database and PubChem were used for bioactive compounds datamining.

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Kibinge, Nelson, Shun Ikeda, Naoaki Ono, Md Altaf-Ul-Amin, and Shigehiko Kanaya. "Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/753428.

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Progress in the “omics” fields such as genomics, transcriptomics, proteomics, and metabolomics has engendered a need for innovative analytical techniques to derive meaningful information from the ever increasing molecular data. KNApSAcK motorcycle DB is a popular database for enzymes related to secondary metabolic pathways in plants. One of the challenges in analyses of protein sequence data in such repositories is the standard notation of sequences as strings of alphabetical characters. This has created lack of a natural underlying metric that eases amenability to computation. In view of this requirement, we applied novel integration of selected biochemical and physical attributes of amino acids derived from the amino acid index and quantified in numerical scale, to examine diversity of peptide sequences of terpenoid synthases accumulated in KNApSAcK motorcycle DB. We initially generated a reduced amino acid index table. This is a set of biochemical and physical properties obtained by random forest feature selection of important indices from the amino acid index. Principal component analysis was then applied for characterization of enzymes involved in synthesis of terpenoids. The variance explained was increased by incorporation of residue attributes for analyses.

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Febriyandi, Nuvandaru Fajar Dzikra, Ahmad Shobrun Jamil, and M. Artabah Muchlisin. "Discovery New Drug Cycela barbata in Alcohol Use Disorder Using Pharmacological Methods." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 194. http://dx.doi.org/10.18860/planar.v3i0.2485.

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Alcohol use disorder (AUD) is a medical condition characterized by an impaired ability to stop or control alcohol use including conditions that some refer to as alcohol abuse, alcohol dependence, alcohol addiction, and the colloquial term, alcoholism. The aim of this research is to find the potential of grass jelly (Cyclea barbata) for treating alcohol. The method used is in silico pharmacological network analysis. Secondary metabolite compound data was obtained from the Knapsack database, prediction of the ability to penetrate the blood brain barrier using the Boiled-Egg method in SwissADME. Prediction of proteins related to C. barbata used SwisstTargetPrediction. Pharmacological network analysis using StringDB and Disease Gene methods. The screening results from KnapSack showed 18 compounds, and only three compounds, namely beta-Cyclanoline, (-)-N-Methylcoclaurine, and (+)-Coclaurine, were predicted to be able to penetrate the blood-brain barrier using Boiled-EGG. From SwissTargetPrediction, 125 proteins related to C. barbata were obtained. From pharmacological network analysis, it was found that 6 proteins were related to alcohol use disorder, namely DRD3, HTR2A, SLC6A3, DRD2, OPRM1, and SLC6A4. So it can be concluded that C. barbata has potential as a plant that can be used to treat AUD.

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Akiyama, Kenji, Eisuke Chikayama, Hiroaki Yuasa, et al. "PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 8, no. 3-4 (2008): 339–45. https://doi.org/10.3233/isb-00362.

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PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research and analysis workflows ranging from metabolome to transcriptome analysis. The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses (SpinAssign for the identification of metabolites by means of NMR, KNApSAcK for searches within metabolite databases). In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting for the analysis of mRNA expression. Use of the tools and database can contribute to the analysis of biological events at the levels of metabolites and gene expression, and we describe one example of such an analysis for Arabidopsis thaliana using the batch-learning self-organizing map (BL-SOM), which is provided via the Web site.

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Book chapters on the topic "KNApSAck database"

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Chen, Rung-Ching, Yun-Hou Huang, and Ming-Hsien Lin. "Solving Unbounded Knapsack Problem Based on Quantum Genetic Algorithms." In Intelligent Information and Database Systems. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12145-6_35.

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Azamimi Abdullah, Azian, M. D. Altaf-Ul-Amin, and Shigehiko Kanaya. "Insight into Knapsack Metabolite Ecology Database: A Comprehensive Source of Species: Voc-Biological Activity Relationships." In Volatile organic compound analysis in biomedical diagnosis applications. Apple Academic Press, 2018. http://dx.doi.org/10.1201/9780429433580-9.

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Okada, Taketo, Farit Mochamad Afendi, Akira Katoh, Aki Hirai, and Shigehiko Kanaya. "Multivariate Analysis of Analytical Chemistry Data and Utility of the KNApSAcK Family Database to Understand Metabolic Diversity in Medicinal Plants." In Biotechnology for Medicinal Plants. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29974-2_18.

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Stahl, Florian, and Gottfried Vossen. "Fair Knapsack Pricing for Data Marketplaces." In Advances in Databases and Information Systems. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-44039-2_4.

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Abbassi, Kamel, and Tahar Ezzedine. "Queries Processing in Wireless Sensor Network." In Wireless Sensor Networks - Design, Deployment and Applications. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.94749.

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For the super-excellence applications used to control the water level in rivers, temperature handles a very large volume of information and does not stop constantly changing. These spatio-temporal data collected by a network of sensors form a set of thematic, integrated, non-volatile and historical data organized to help decision-making. Usually this process is performed with temporal, spatial and spatiotemporal queries. This in turn increases the execution time of the query load. In the literatures, several techniques have been identified such as materialized views (MV), indexes, fragmentation, scheduling, and buffer management. These techniques do not consider the update of the request load and the modification at the database level. In this chapter, we propose an optimal dynamic selection solution based on indexes and VMs. the solution is optimal when it meets the entire workload with a reasonable response time. The proposed approach supports modification at the database level and at the workload level to ensure the validity of the optimal solution for this the knapsack algorithm was used.

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Kumar, Rajeev. "Algorithms for Selecting the Optimum Dataset While Providing Personalized Privacy and Compensation to its Participants." In Research Anthology on Privatizing and Securing Data. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-8954-0.ch033.

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The privacy preserving microdata sharing literature has proposed several techniques that allow a database administrator to share a dataset in a privacy preserving manner. This paper considers the implications of adding a market layer to that setting. In this setting, individuals (data providers) can receive a market-determined compensation in exchange for their information while they also receive a personalized privacy protection. The computational burdens of satisfying a variety of privacy requirements of individuals (sellers) and dataset requirements of the data receiver (buyer) are analyzed in this paper. The author presents a polynomial time reformulation procedure that proves that the “optimum information product” creation problem reduces to multiple-choice knapsack problem, which is a weakly NP hard problem. The problem of various instance sizes is solved using FICO Xpress 7.0 optimization software. The insights presented in the paper can be utilized for creating a market of individual information in different settings.

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Conference papers on the topic "KNApSAck database"

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Wedashwara, Wirarama, Shingo Mabu, Masanao Obayashi, and Takashi Kuremoto. "Implementation of genetic network programming and knapsack problem for record clustering on distributed database." In 2014 53rd Annual Conference of the Society of Instrument and Control Engineers of Japan (SICE). IEEE, 2014. http://dx.doi.org/10.1109/sice.2014.6935234.

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