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Journal articles on the topic 'KNApSAck database'

Author: Grafiati

Published: 5 June 2025

Last updated: 16 July 2025

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1

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 datab

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2

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 didistribusi

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4

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 KNA

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6

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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8

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

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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.

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10

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 Sear

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11

Primadhanty. R. S. Bhadra, Mardiana, Ahmad Fiqri, Ummi Rinandari, Didik H. Utomo, and Muhammad Eko Irawanto. "Analisis In Silico Potensi Minyak Kedelai (Glycine max) dalam Terapi Dermatitis Atopik." MEDICINUS 34, no. 2 (2021): 21–25. http://dx.doi.org/10.56951/medicinus.v34i2.63.

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Minyak kedelai (Glycine max) mengandung berbagai fitokimia bioaktif seperti phenolic acid, flavonoid, isoflavone, saponin, phytosterol, dan sphingolipid yang diduga memiliki manfaat pada pengobatan dermatitis atopik (DA). Penelitian ini bertujuan untuk mengevaluasi potensi kandungan dari minyak kedelai menggunakan analisis in silico secara komputasional pada pengobatan dermatitis atopik. Senyawa aktif dari minyak kedelai diekstraksi dari database KNApSAcK. Hasil yang didapatkan yaitu terdapat potensi bioaktivitas minyak kedelai sebagai imunosupresan, antiinflamasi, perbaikan barrier kulit, ant

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Wijaya, Sony Hartono, Husnawati Husnawati, Farit Mochamad Afendi, et al. "Supervised Clustering Based on DPClusO: Prediction of Plant-Disease Relations Using Jamu Formulas of KNApSAcK Database." BioMed Research International 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/831751.

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Indonesia has the largest medicinal plant species in the world and these plants are used as Jamu medicines. Jamu medicines are popular traditional medicines from Indonesia and we need to systemize the formulation of Jamu and develop basic scientific principles of Jamu to meet the requirement of Indonesian Healthcare System. We propose a new approach to predict the relation between plant and disease using network analysis and supervised clustering. At the preliminary step, we assigned 3138 Jamu formulas to 116 diseases of International Classification of Diseases (ver. 10) which belong to 18 cla

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13

Ginoga, Muh Fadhil Al-Haaq, Wisnu Ananta Kusuma, and Mushthofa Mushthofa. "Prediksi Interaksi Drug Target pada Gen Kanker Menggunakan Metode Lasso-XGBoost." Jurnal Teknologi Informasi dan Ilmu Komputer 10, no. 3 (2023): 531–42. http://dx.doi.org/10.25126/jtiik.20231036603.

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Pengobatan kanker saat ini sering dilakukan dengan kemoterapi menggunakan obat kimia dan dapat menyebabkan efek samping. Alternatif pengobatan dapat menggunakan senyawa herbal yang diketahui memiliki efek samping lebih sedikit. Analisis Drug Target Interaction (DTI) dapat dilakukan untuk mengetahui interaksi senyawa herbal terhadap protein kanker. Pada penelitian ini dilakukan perancangan model prediksi DTI dengan melakukan seleksi fitur pada dataset menggunakan Least Absolute Shrinkage and Selection Operator (LASSO) lalu dilakukan penyeimbangan data dengan Synthetic Minority Oversampling Tech

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Ginoga, Muh Fadhil Al-Haaq, Wisnu Ananta Kusuma, and Mushthofa Mushthofa. "Prediksi Interaksi Drug Target pada Gen Kanker Menggunakan Metode Lasso-XGBoost." Jurnal Teknologi Informasi dan Ilmu Komputer 10, no. 3 (2023): 531–42. https://doi.org/10.25126/jtiik.2023106603.

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Pengobatan kanker saat ini sering dilakukan dengan kemoterapi menggunakan obat kimia dan dapat menyebabkan efek samping. Alternatif pengobatan dapat menggunakan senyawa herbal yang diketahui memiliki efek samping lebih sedikit. Analisis Drug Target Interaction (DTI) dapat dilakukan untuk mengetahui interaksi senyawa herbal terhadap protein kanker. Pada penelitian ini dilakukan perancangan model prediksi DTI dengan melakukan seleksi fitur pada dataset menggunakan Least Absolute Shrinkage and Selection Operator (LASSO) lalu dilakukan penyeimbangan data dengan Synthetic Minority Oversampling Tech

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15

Saputro, Dominyda Vebrianto, Ahmad Shobrun Jamil, M. Artabah Muchlisin, and Irsan Fahmi Almuhtarihan. "A Network Pharmacology of Lemongrass (Cymbopogon citratus) on COVID-19 Cases." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 49. http://dx.doi.org/10.18860/planar.v3i0.2471.

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Various ways and treatment efforts are carried out to avoid the severe impact of COVID-19 cases, one of which is using plants as natural immunomodulatory agents. One of the plants that is proven to act as a natural immunomodulator is lemongrass (Cymbopogon citratus). This study aimed to determine the protein tissue associated with the body's immune system activated by C. citratus. The secondary metabolites of C. citratus were identified using the KNApSAck and Dr. Duke databases. Target proteins associated with plant-secondary metabolite compounds from the SwissTargetPrediction database and imm

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16

Huma, Qureshi, Anwar Tauseef, Khan Sadiqullah, Fatimah Hina, and Waseem Muhammad. "Phytochemical constituents of Broussonetia papyrifera (L.) L'He'r. ex Vent: An overview†." Journal of Indian Chemical Society Vol. 97, Jan 2020 (2020): 55–65. https://doi.org/10.5281/zenodo.5651019.

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Department of Biological Sciences (Botany Program), Gomal University, Dera Ismail Khan-29050, Pakistan Department of Botany, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi-46300, Pakistan <em>E-mail</em>: humaqureshi8@gmail.com Department of Environmental Science, Gomal University, Dera Ismail Khan-29050, Pakistan Department of Biology, Allama Iqbal Open University, Islamabad-46000, Pakistan <em>Manuscript received online 15 October 2019, revised and accepted 06 January 2020</em> Phytochemistry is an important field of plant biology with a number of applied research applications. Wh

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17

Setiani, Lusi Agus, Wisnu Ananta Kusuma, and Fitria Nadiatul Rizal. "Exploring the Potential Mechanism of “X” Jamu Capsule in Treating Hypertension Based on Network Pharmacology." FITOFARMAKA: JURNAL ILMIAH FARMASI 14, no. 2 (2024): 99–109. https://doi.org/10.33751/jf.v14i2.11.

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Jamu is a traditional medicine derived from plants, animals, minerals, and galenic preparations that are used empirically as a treatment. Hypertension is a condition when the systolic blood pressure is > 140 mmHg and the diastolic blood pressure is > 90 mmHg. The purpose of this research is to describe the mechanism of action of Jamu which consists of six plants, namely Apium Graveolens, Orthosiphon aristatus, Imperatae cylindrica, Phyllanthus niruri, Centella asiatica, and Curcuma xanthorrhiza as antihipertensive using network pharmacology because the herbs are formula with multi-compon

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18

Adianingsih, Oktavia Rahayu, Fifi Farida Fajrin, and Christopher Kuncoro Johan. "Exploring the mechanism of Glycyrrhiza glabra and Curcuma domestica against skin photoaging based on network pharmacology." Indonesian Journal of Biotechnology 29, no. 2 (2024): 98. http://dx.doi.org/10.22146/ijbiotech.93332.

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Excessive exposure to UV radiation results in skin photoaging, which may be prevented or treated using natural plant compounds. Herbal cosmetics and medicines have grown in popularity due to the abundance of relatively safe compounds. This research aims to explore the network pharmacology of Glycyrrhiza glabra (GG) and Curcuma domestica (CD) against skin photoaging. Active compounds from GG‐CD were sourced from databases including TCSMP, KnapSack, TCMID, and published literature, while disease targets were collected from GeneCards and OMIM databases. The STRING database was utilized to constru

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Oishi, Takashi, Ken-ichi Tanaka, Takuya Hashimoto, et al. "An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites." Plant Biotechnology 26, no. 1 (2009): 167–74. http://dx.doi.org/10.5511/plantbiotechnology.26.167.

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20

Liu, K., Md Altaf-Ul-Amin, A. A. Abdullah, A. H. Morita, M. Shiraishi, and S. Kanaya. "A novel plant classification method based on similarities in chemical structures of metabolite contents obtained from the KNApSAcK database." Acta Horticulturae, no. 1169 (July 2017): 139–50. http://dx.doi.org/10.17660/actahortic.2017.1169.21.

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21

Kumar, Rajeev. "Algorithms for Selecting the Optimum Dataset While Providing Personalized Privacy and Compensation to its Participants." International Journal of Operations Research and Information Systems 8, no. 4 (2017): 43–58. http://dx.doi.org/10.4018/ijoris.2017100103.

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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

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Supratik, Adhikary, and Aditi Nayak Dr. "In Silico Analysis of Secondary Metabolite Biosynthesis Clusters in the Genome of Panicum virgatum." International Journal of Scientific Development and Research 8, no. 7 (2023): 552–63. https://doi.org/10.5281/zenodo.8374134.

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A biosynthetic gene cluster (BGC) is a group of genes in a genome that collectively encode the enzymes responsible for producing a specific natural product, such as a secondary metabolite or a bioactive compound with diverse biological activities, including antibiotics, antifungals, antiviral agents. Understanding the structure and function of these biosynthetic gene clusters is important for developing new pharmacological compounds. By studying these clusters, it would be beneficial in identifying the potential targets for drug development and strategies to prevent the spread of antibiotic re

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Arrohmah, Robiatus Sholichah, Afina Anjani Ibtisam, Siti Malihatus Sa’adah, Fensy Rania Putri, and Fitriyah Fitriyah. "Bioactivity mapping of secondary metabolite compounds of Pandanus amaryllifolius leaves as anti-inflammatory using in silico." Journal of Natural Sciences and Mathematics Research 9, no. 1 (2023): 50–59. http://dx.doi.org/10.21580/jnsmr.2023.9.1.16215.

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Inflammation is one of the primary responses of the immune system to infection and irritation. Anti-inflammatory drugs generally cause side effects. Anti-inflammatory developed by reducing side effects use many natural materials such as plants. The parts of the plant used include fruits, leaves, stem bark, rhizomes, and flowers. One of the plants that can be used as an anti-inflammatory is Pandanus amaryllifolius. P. amaryllifolius leaves contain several materials, such as flavonoids, alkaloids, saponins, tannins, polyphenols, and dyes. This study aimed to determine the anti-inflammatory poten

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Ramadhan, Dwi Syah Fitra, Taufik Muhammad Fakih, and Arfan Arfan. "Activity Prediction of Bioactive Compounds Contained in Etlingera elatior Against the SARS-CoV-2 Main Protease: An In Silico Approach." Borneo Journal of Pharmacy 3, no. 4 (2020): 235–42. http://dx.doi.org/10.33084/bjop.v3i4.1634.

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The COVID-19 pandemic has become a serious problem today, with its prevalence increasing every day. The SARS-CoV-2 main protease (MPro) is a promising therapeutic target to inhibit replicating and spreading the virus that causes COVID-19. The compounds contained in the Etlingera elatior plant has the potential. This study aimed to examine the compounds' activity in E. elatior against SARS-CoV-2 MPro using in silico methods. A total of seven compounds contained in E. elatior were obtained from the Knapsack database. The compounds were then docked into the SARS-CoV-2 MPro receptor's active site

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Hadi, Samsul, Deni Setiawan, Kunti Nastiti, Muhammad R. Ridha, and Yustinus Maladan. "Screening for Alcohol Dehydrogenase Inhibitors from Dendrobium Using the In-silico Method." INTERNATIONAL JOURNAL OF DRUG DELIVERY TECHNOLOGY 13, no. 02 (2022): 568–75. http://dx.doi.org/10.25258/ijddt.13.2.17.

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The incidence of acute kidney failure has become a concern and needs preventive action as soon as possible. Fomepizole and ethanol are the treatment options for acute kidney injury (AKI). The development approach is carried out through structural approaches to fomepizole or ethanol, anti-inflammatory activity, and chelate formation. Dendrobium is a potential plant with various activities and many secondary metabolites such as bibenzyl, alkaloids, sesquiterpenes, and phenanthrenes. This study aims to find compounds that have the potential to be ADH inhibitors from Dendrobium using the in-silico

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Annisadila, Shindy, Ahmad Shobrun Jamil, and M. Artabah Muchlisin. "Bioavaibility Evaluation and Molecular Docking of Cananga odorata Plant as Anti-Inflammatory Potential Against Crohn’s Disease." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 126. http://dx.doi.org/10.18860/planar.v3i0.2478.

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Crohn's disease is a chronic inflammatory bowel disease (IBD) that affects the digestive tract. One of the potential targets for this disease is LRRK2. Kenanga (Cananga odorata) is known to have anti-inflammatory effects. The study aims to identify the potential of the secondary metabolite compounds found in C. odorata against LRRK2 in silico. The KnapSack database was used to identify the secondary metabolite compounds of C. odorata, SwissADME was used to find the compound with high bioavailability with the Boiled-EGG method, and PyRx with the AutoDock was used for molecular docking. Accordin

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Prasetyorini, Budi Eko, Arie Kusumawardani, Fatimah Fitriani, Putri Ooktriana Rachman, Nathania Amelinda, and Anggia Ramadhani. "Analisis <i>In Silico</i> Senyawa Aktif Batang Kayu Bajakah (<i>Spatholobus littoralis</i> Hassk) Sebagai Terapi Psoriasis." Herb-Medicine Journal 5, no. 1 (2022): 26. http://dx.doi.org/10.30595/hmj.v5i2.12744.

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Background : Innovative topical psoriasis therapy continues to be developed, Spatholobus littoralis Hassk or Bajakah has antipsoriatic activity so can be used as a topical herbal medicine in reducing the severity of psoriasis. In silico is a computational experiment which is analogous to biological experiments in vivo and in vitro. Objective : To evaluate content of Spatholobus littoralis Hassk using in silico analysis in the treatment of psoriasis. Methods : The active compound Spatholobus littoralis Hassk extracted from the knapsack database. The simplified molecular input line entry system

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Setiawan, Risma Ayu, Ahmad Shobrun Jamil, Siti Rofida, and M. Artabah Muchlisin. "Melaleuca leucadendra Pharmacological Network for Identifying Potential Target of Alcohol Dependence." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 111. http://dx.doi.org/10.18860/planar.v3i0.2477.

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Melaleuca leucadendra (ML) contains a compound that is potentially a candidate for alcohol dependence. Alcohol dependence is defined by desire, tolerance, anxiety with alcohol, and continuing to drink even though the consequences are dangerous. The study aims to analyze the potential of the ML compound content for alcohol dependence therapy within silico-based pharmacological chain analysis. ML compound data is obtained from the Knapsack database, screening of absorption, distribution, metabolism, and excretion (ADME) of the compounds ML with SwissADME, prediction of the protein of the target

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Wijaya, Johanna Fransiska, Linda Chiuman, Hariyadi Dharmawan Syahputra, et al. "Investigation of Potential Molecular Targets of Zanthoxylum acanthopodium in Ovarian Cancer Using Network Pharmacology Assessments." Journal of Multidisciplinary Applied Natural Science 5, no. 2 (2025): 630–43. https://doi.org/10.47352/jmans.2774-3047.268.

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Ovarian cancer is a serious disease that affects the ovaries, and its early detection is challenging due to vague symptoms often dismissed as minor ailments. Currently, natural sources have gained attention for their potential role in anticancer treatment. This study aimed to utilize network pharmacology to explore the potential targets and mechanisms of Zanthoxylum acanthopodium in the treatment of ovarian cancer. This study utilized the KNApSAcK and Swiss Target Prediction to identify active compounds and target genes. Additionally, ovarian cancer-specific target genes were sourced from the

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Yongpisanphop, J. "Searching for a plant species having a potent bioherbicide using in silico approach." Research Journal of Chemistry and Environment 26, no. 1 (2021): 97–103. http://dx.doi.org/10.25303/2601rjce97103.

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Toxic herbicide residue in the environment is one of the most important problems in the world, especially in the agricultural country. To solve this problem, an effectively new bioherbicide needs to be discovered urgently. This motivated to search the novel bioherbicide. In silico technique has been accepted as a promising tool to discover new active compounds. Based on 2D structural similarity, 18 new natural compounds were obtained from the KNApSAcK database. Among the structural leads, 12 natural phyto-compounds were selected to calculate the lowest free energy of binding value using molecu

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Anwar, La Ode Muhammad, Anas Kiki Anugrah, Embriana Dinar Pramestyani, et al. "Studi Farmakokinetik dan Toksisitas Senyawa Biji Jintan Hitam (Nigella sativa)." Jurnal Mandala Pharmacon Indonesia 10, no. 2 (2024): 736–42. https://doi.org/10.35311/jmpi.v10i2.661.

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Studi farmakokinetik dan toksisitas merupakan salah satu parameter dalam pengembangan obat. Parameter farmakokinetik meliputi nilai absorbs, distribusi, metabolisme dan eliminasi obat sedangkan nilai toksisitas merupakan factor keamanan pada suatu komponen senyawa atau sediaan. Tujuan dari penelitian ini adalah untuk melihat nilai farmakokinetik dan toksisitas pada tanaman jintan hitam (Nigella sativa). Database senyawa diperoleh pada situs Take out "JAMU" of KNApSAcK dan dianalsis kode SMILES pada platfrom PubChem. Selanjutnya dilakukan analisis farmakokinetik dan toksisitas menggunakan situs

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Widyaswari, Meidyta Sinantryana, Iis Noventi, and Herdiantri Supriyana. "Anti-eczema Mechanism of Action of Nigella sativa for Atopic Dermatitis: Computer-aided Prediction and Pathway Analysis Based on Protein-chemical Interaction Networks." Biomolecular and Health Science Journal 2, no. 2 (2019): 68. http://dx.doi.org/10.20473/bhsj.v2i2.15007.

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Introduction: Black cumin (Nigella sativa) is widely used to treat various diseases. It is also believed to relief skin conditions accompanied by itching symptom, such as atopic dermatitis (AD) or eczema. However, the anti-eczema mechanism of action is still unclear. The aims of this syudy was to identify anti-eczema mechanism of action of N. sativa for AD using computer aided prediction and pathway analysis based on protein-chemical networks. Methods: We utilized dataset consisting chemical compounds of N. sativa from KNApSAcK. It is a comprehensive species-metabolite relationship database. U

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Handayani, Vitri Aprilla, Farit Mochamad Afendi, and Wisnu Ananta Kusuma. "Penguraian Mekanisme Kerja Jamu Berdasarkan Jejaring Bahan Aktif-Protein Target-Gene Ontology." Jurnal Jamu Indonesia 1, no. 3 (2016): 18–28. http://dx.doi.org/10.29244/jji.v1i3.21.

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Jamu merupakan obat tradisional Indonesia. Pada dasarnya obat herbal yang dibuat dari bahan-bahan alami yang diambil dari beberapa bagian dari tanaman obat yang mengandung beberapa zat dan senyawa yang penting dan bermanfaat bagi tubuh. Sejauh ini, khasiat untuk beberapa jenis jamu secara empiris telah terbukti. Dalam peneitian ini, kami bermaksud untuk menguraikan mekanisme kerja jamu menggunakan pendekatan komputasi. Penelitian ini berfokus pada ramuan jamu type 2 diabetesyang terdiri dari empat tanaman, yaitu: jahe, bratawali, sembung, dan pare. Kerangka analisis awal dengan membentuk 3 kom

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Aprilla Handayani, Vitri, Farit Mochamad Afendi, and Wisnu Ananta Kusuma. "Penguraian Mekanisme Kerja Jamu Berdasarkan Jejaring Bahan Aktif-Protein Target-Gene Ontology." Jurnal Jamu Indonesia 1, no. 3 (2016): 18–28. http://dx.doi.org/10.29244/jjidn.v1i3.30640.

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Jamu merupakan obat tradisional Indonesia. Pada dasarnya obat herbal yang dibuat dari bahan-bahan alami yang diambil dari beberapa bagian dari tanaman obat yang mengandung beberapa zat dan senyawa yang penting dan bermanfaat bagi tubuh. Sejauh ini, khasiat untuk beberapa jenis jamu secara empiris telah terbukti. Dalam peneitian ini, kami bermaksud untuk menguraikan mekanisme kerja jamu menggunakan pendekatan komputasi. Penelitian ini berfokus pada ramuan jamu type 2 diabetesyang terdiri dari empat tanaman, yaitu: jahe, bratawali, sembung, dan pare. Kerangka analisis awal dengan membentuk 3 kom

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Mardiana, Primadhanty B, Adniana N, et al. "Analisis In Silico pada VCO untuk Terapi Dermatitis Atopik." MEDICINUS 33, no. 3 (2020): 32–37. http://dx.doi.org/10.56951/medicinus.v33i3.74.

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Latar belakang: Analisis in silico digunakan pada tahap awal penelitian dalam penemuan obat baru untuk efisiensi biaya dan waktu. Virgin Coconut Oil (VCO) merupakan salah satu pilihan terapi pada kasus dermatitis atopik karena memiliki fungsi memperbaiki barrier kulit dan antiinflamasi. Tujuan: Untuk mengevaluasi kandungan VCO menggunakan analisis in silico secara komputasional pada pengobatan dermatitis atopik. Metode: Senyawa aktif Cocos nucifera yang diekstraksi dari database KNApSAcK diprediksi secara eksperimental dan dianalisis secara komputasi menggunakan Simplified Molecular-Input Line

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Maretha, Tri Luthfiana, Ahmad Shobrun Jamil, Siti Rofida, and M. Artabah Muchlisin. "Network Pharmacology Analysis of Cananga odorata as a Treatment for Anxiety Disorders." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 137. http://dx.doi.org/10.18860/planar.v3i0.2479.

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Anxiety disorder is a psychological disorder associated with the existence of mental disorders and experiencing constant anxiety. In C. odorata, part of the flower has the potential as a sedative for the nervous system and for dealing with anxiety. The study aims to analyze the potential compound content in Cananga odorata for treating anxiety disorders with In silico-based pharmacological network analysis. CO compound data from the KNApSAck database, Absorption, Distribution, Metabolism, and Excretion (ADME) screening using SwissADME, predicted target proteins using Swiss Target Prediction, G

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Jamil, Ahmad Shobrun, Sri Widyarti, Meddy Setiawan, and Muhaimin Rifa’i. "The pharmacological network of Tinospora cordifolia: Its role in regulating ınflammation and cathelicidin production." Journal of Research in Pharmacy 29, no. 3 (2024): 903–17. https://doi.org/10.12991/jrespharm.1693737.

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This study aims to promote a pharmacological network strategy to investigate the potential antiinflammatory activity and molecular mechanisms of the bioactive compounds in Tinospora cordifolia (TC) for controlling inflammation and regulating the production of the antimicrobial peptide cathelicidin. Using the Knapsack database and several recent research findings, SwissADME, PubChem, and PASS Online, we screened the drug-likeness of various TC compounds. Utilizing the SwissTargetPrediction, String-DB, GeneCards, and Venny Diagram, we identified 468 potential targets related to inflammation targ

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Naraevskii, О., and T. Chernomorova. "On the optimal use of material for manufacturing products by a metal construction plant." Bulletin of Science and Practice, no. 4 (April 15, 2017): 115–22. https://doi.org/10.5281/zenodo.546280.

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As part work, the task of optimising the production of road safety products at the North Caucasian Plant of Metal Constructions LLC is being solved. As a conceptual model, the problem of a backpack from decision theory has been chosen. In this paper, we use and compare the results of two methods: a simple search and a method of branches and boundaries. It is necessary to make the maximum number of road signs of a certain type from sheets of metal of various dimensions while minimising production waste. The original algorithm executed on the Oracle 11g database platform in the built-in PL/SQL l

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Widyananda, Muhammad Hermawan, Septian Tri Wicaksono, Kurnia Rahmawati, et al. "A Potential Anticancer Mechanism of Finger Root (Boesenbergia rotunda) Extracts against a Breast Cancer Cell Line." Scientifica 2022 (September 5, 2022): 1–17. http://dx.doi.org/10.1155/2022/9130252.

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Breast cancer is the most common type of cancer women suffer from worldwide in 2020 and the 4th leading cause of cancer death. Boesenbergia rotunda is an herb with high potential as an anticancer agent. This study explores the potential bioactive compounds in B. rotunda as anti-breast cancer agents using in silico and in vitro approaches. The in silico study was used for active compound analysis, selection of anticancer compound candidates, prediction of target protein, functional annotation, molecular docking, and molecular dynamics simulation, respectively. The in vitro study was conducted b

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Khoirunnisa, Azka, Ahmad Shobrun Jamil, and Muhammad Artabah Muchlisin. "Network Pharmacology Analysis of Secondary Metabolites of Ciplukan (Physalis angulata L.) Against Lung Cancer." Majalah Farmaseutik 20, no. 2 (2024): 282. http://dx.doi.org/10.22146/farmaseutik.v20i2.96275.

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Lung cancer is the most common and high-risk type of cancer. Ciplukan (Physalis angulata L.) has antibacterial, anti-inflammatory, and anticancer activities, as well as cytotoxic ability and inhibits cancer cell growth. Research that discusses the molecular cellular mechanism of P. angulata's potential as an anti-lung cancer has not been widely informed, especially on the network pharmacology aspect of this plant's active compounds. This study reveals the prediction of the molecular mechanism of active compounds of P. angulata as anti-lung cancer using several tools including: Compound databas

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Rahayu, Premy Puspitawati, Manik Eirry Sawitri, Dwi Setiawan, and Citra Nurma Yunita. "Interaction of Sambiloto (Andrographis paniculata) Bioactive Compound with Milk Protein (Whey and Casein) Through Molecular Docking and Molecular Dynamics Simulation as a Basis for Encapsulation." Jurnal Penelitian Pendidikan IPA 10, no. 7 (2024): 4129–38. http://dx.doi.org/10.29303/jppipa.v10i7.7696.

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This research aims for developing immune-boosting products necessary. The active ingredient in Andrographis paniculate (AP) acts as an immunostimulant which can improve the work of the immune system. The first stage of research was a collection of bioactive compounds from KnapSack database of Kanaya, Dr. Duke's Phytochemical and Ethnobotanical were compiled and selected based on the online pass results of each bioactive compound as an immunomodulator and 10 active compounds were obtained which will be continued. The second stage of research was a docking molecular between whey proteins (β-lact

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Liyaajul, Pratasyah, Miftahul Mushlih, Chylen Setiyo Rini, and Jamilatur Rohmah. "Analysis Of The Inhibitory Ability Of Spike Attachment Of The Delta Variant Of Sars Cov-2 With Ace2 By The Active Compound In Turmeric (Curcuma longa L.) In Silico." Medicra (Journal of Medical Laboratory Science/Technology) 6, no. 1 (2023): 19–24. http://dx.doi.org/10.21070/medicra.v6i1.1703.

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Turmeric (Curcuma longa L.) is an herbal plant that has many benefits as a treatment, including during the COVID-19 pandemic, one of the mechanisms of inhibition of SARS CoV-2 is to inhibit the attachment of ACE2 with Spike. The binding of the spike protein to the ACE2 receptor will produce conformational changes in the S protein, this study was conducted using an in silico method (computational analysis) which aims to determine the potential efficacy of Turmeric and its effectiveness in inhibiting the Delta variant of SARS CoV-2. The active compound contained in Turmeric (Curcuma longa L. ) o

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Awwaluddin, Faiznanda, Ahmad Shobrun Jamil, Siti Rofida, and M. Artabah Muchlisin. "The Therapeutic Role of Olea europaea in Alcohol Dependence Base in Network Pharmacology Analysis." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 201. http://dx.doi.org/10.18860/planar.v3i0.2486.

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Alcohol dependence is a state of alcohol becoming a vital part of the life of a person who consumes it; when discontinued, it can lead to a wide range of physical and mental health disorders as well as a decrease in life productivity in people with alcohol dependence. Olea Europaea (OE) is a plant capable of treating alcohol dependence. The method used in silico-based pharmacological grid analysis to determine the ability of the OE compound to treat alcohol dependence. EO compound data is obtained from the KnapSack database, absorption, distribution, metabolism, and excretion (ADME) screening

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Fauzan, Irfan Anwar, Ditta Putri Kumalasari, and Nisrina Fitri Nurjannah. "In Silico Screening of Ruellia tuberosa Phytochemicals as Neuroimmune-Modulating Drug Candidates for Multiple Sclerosis Therapy." International Journal of Research and Review 12, no. 6 (2025): 536–40. https://doi.org/10.52403/ijrr.20250661.

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Multiple sclerosis (MS) is a chronic autoimmune disease characterized by neuroinflammation, demyelination, and progressive neurological decline. Current pharmacotherapies offer limited efficacy and often induce adverse effects, highlighting the need for safer, multi-target alternatives. This study employed an in silico approach to evaluate phytochemical compounds from Ruellia tuberosa as potential neuroimmune-modulating drug candidates for MS therapy. Five bioactive compounds, which are hentriacontane, nonacosane, campesterol, β-sitosterol, and stigmasterol, were identified through the KNApSAc

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Widyananda, Muhammad Hermawan, Coni Anggie Kurniasari, Fajar Mustika Alam, et al. "Exploration of Potentially Bioactive Compounds from Fingerroot (Boesenbergia rotunda L.) as Inhibitor of Atherosclerosis-Related Proteins (CETP, ACAT1, OSC, sPLA2): An in silico Study." Jordan Journal of Pharmaceutical Sciences 16, no. 3 (2023): 550–64. http://dx.doi.org/10.35516/jjps.v16i3.1609.

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Boesenbergia rotunda L., commonly known as fingerroot, is recognized as one of Indonesia's medicinal plants with significant potential for treating various diseases, including atherosclerosis. This study aims to analyze the anti-atherosclerosis potential of bioactive compounds found in fingerroot by assessing their inhibitory effects on four proteins associated with atherosclerosis (CETP, ACAT1, OSC, and sPLA2). Bioactive compounds from B. rotunda were retrieved from the KnapSack database. The drug-likeness properties were predicted using the SwissADME web server, and the bioactivity of the co

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Федорец, О. В., та Н. С. Солошенко. "О практической значимости информетрической модели Брэдфорда для прогнозирования рассеяния статей и оптимизации отбора журналов". Научно-техническая информация. Серия 2: Информационные процессы и системы, № 1 (1 січня 2024): 34–44. https://doi.org/10.36535/0548-0027-2024-01-3.

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Исследовано рассеяние статей в реферативной базе данных ВИНИТИ РАН в период 2020-2022 гг. на примере трёх тематических фрагментов: Химия и химическая технология, Машиностроение, Металлургия и сварка. Для вычисления количества журналов в третьей зоне рассеяния использовались математические формулировки С. Брэдфорда и Б. Викери. Сделан вывод, что закон рассеяния публикаций Брэдфорда-Викери позволяет прогнозировать минимальное количество журналов, охватывающих более 90% статей по определенной тематике. Оптимизация отбора журналов сведена к известной задаче о рюкзаке (ранце), для решения которой п

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Ikeda, Shun, Takashi Abe, Yukiko Nakamura, et al. "Systematization of the Protein Sequence Diversity in Enzymes Related to Secondary Metabolic Pathways in Plants, in the Context of Big Data Biology Inspired by the KNApSAcK Motorcycle Database." Plant and Cell Physiology 54, no. 5 (2013): 711–27. http://dx.doi.org/10.1093/pcp/pct041.

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Fatiningtyas, Fairuz Andini, Riswanto Napitupulu, Amarila Malik, and Is Helianti. "In Silico and In Vitro Inhibitory Activity of Indonesian Herbal Compound Extracts against SARS-COV-2 Recombinant Papain-Like Protease." HAYATI Journal of Biosciences 32, no. 2 (2024): 356–66. https://doi.org/10.4308/hjb.32.2.356-366.

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The SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and a promising target for drug discovery. This study explored the inhibitory potential of compounds from Indonesia herbals Butterfly pea flower (Clitoria ternatea L), Star fruit leaves (Averrhoa carambola L.), and Java plum leaves (Syzygium cumini (L.) Skeels) against PL pro through molecular docking and in vitro assays. The molecular docking method utilized the target protein PLpro (PDB ID: 7CMD), with the native ligand obtained from compounds identified in these plant extracts. The compounds were identified using

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Yasmin, Rafida, Wulan Usfi Mafiroh, Anggiresti Kinasih, Aulia Noor Ramadhani, Rachmi Putri, and Endang Semiarti. "Potential of Orchids Secondary Metabolites as Anti-Cancer and Antimicrobial Based on Prediction of Phytochemical Activity with Online PASS-Software." Journal of Agromedicine and Medical Sciences 8, no. 1 (2022): 25. http://dx.doi.org/10.19184/ams.v8i1.26848.

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Abstract Orchidology is part of the branch of botany, it deals with a large family of monocotyledonous plants, Orchidaceae. Orchids have been used as traditional herbal medicines in Indonesia which are believed to be antimicrobial and anti-cancer. Orchids are able to produce secondary metabolites as their protective agent due to the extreme environment. Orchids have great diversity and potential to be the object of research, not only in experimental studies but also in a computational studies like in silico. Nowadays, molecular or metabolite data are available on the official-standard we

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Askar, Muhammad. "Computational quest to inhibit enoyl-acyl carrier protein reductase (InhA) enzyme in Mycobacterium tuberculosis from Lannea coromandelica (Houtt.) Merr. metabolite via molecular docking and dynamics." Pharmacia 71 (August 2, 2024): 1–10. http://dx.doi.org/10.3897/pharmacia.71.e129151.

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This research is a computational exploration to look for natural compounds that can inhibit enoyl-acyl carrier protein reductase (InhA) enzyme from Mycobacterium tuberculosis (MTB). One of Indonesia’s native plants that has been reported to inhibit InhA from MTB is the Lannea coromandelica (Houtt.) Merr., known to contain various active metabolites. However, the molecular activity of the metabolites has not been determined. The aim of this research is the discovery and testing computationally of the binding of metabolites from Lannea coromandelica (Houtt.) Merr. The metabolite ligands are obta

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