Relevant bibliographies by topics / Reverse docking

Contents

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

Academic literature on the topic 'Reverse docking'

Author: Grafiati
Published: 7 July 2024

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Journal articles on the topic "Reverse docking"

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Soto Zuluaga, Juan Pablo, Marcus Thiell, and Rosa Colomé Perales. "Reverse cross-docking." Omega 66 (January 2017): 48–57. http://dx.doi.org/10.1016/j.omega.2016.01.010.

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Listyani, Tiara Ajeng, and Rina Herowati. "Analisis Docking Molekuler Senyawa Derivat Phthalimide sebagai Inhibitor Non-Nukleosida HIV-1 Reverse Transcriptase." Jurnal Farmasi Indonesia 15, no. 2 (2018): 123–34. http://dx.doi.org/10.31001/jfi.v15i2.445.

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Senyawa derivat phthalimide dilaporkan sebagai kelas baru inhibitor nonnukleosida reverse transcriptase. Analisis docking molekuler senyawa derivat phthalimide terhadap enzim reverse transcriptase diperlukan untuk mengetahui afinitas dan pola interaksi antara senyawa di atas dengan enzim reverse transcriptase.
 Senyawa derivat phthalimide dioptimasi geometri menggunakan perangkat lunak VegaZZ selanjutnya dilakukan dengan cara preparasi target, preparasi ligan, validasi metode docking, dan analisis docking menggunakan PyRx-Python 0.8 - AutoDock Vina sehingga didapatkan interaksi ligan dengan target, energi bebas pengikatan, ikatan hidrogen, dan pola interaksi. Pola interaksi dilihat dari tiga puluh tiga senyawa derivat phthalimide dengan enzim reverse transcriptase menunjukkan ikatan hidrogen dengan asam amino Lys101 dimana interaksi tersebut mirip dengan interaksi senyawa TIBO R 86183 yang merupakan ligan asli protein target.
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Seal, Abhik, Riju Aykkal, and Mriganka Ghosh Ghosh. "Docking study of HIV-1 reverse transcriptase with phytochemicals." Bioinformation 5, no. 10 (2011): 430–39. http://dx.doi.org/10.6026/97320630005430.

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Park, Kichul, and Art E. Cho. "Using reverse docking to identify potential targets for ginsenosides." Journal of Ginseng Research 41, no. 4 (2017): 534–39. http://dx.doi.org/10.1016/j.jgr.2016.10.005.

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DA SILVA, CARLOS H. T. P., IVONE CARVALHO, and CARLTON A. TAFT. "MOLECULAR DYNAMICS, DOCKING, DENSITY FUNCTIONAL, AND ADMET STUDIES OF HIV-1 REVERSE TRANSCRIPTASE INHIBITORS." Journal of Theoretical and Computational Chemistry 05, no. 03 (2006): 579–86. http://dx.doi.org/10.1142/s0219633606002441.

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Molecular dynamics, density functional with correlation, as well as docking studies of inhibitors of HIV-1 reverse transcriptase (RT) are reported. We propose in this work a novel potential HIV-1 RT inhibitor (RTI), which theoretically appears to bind in a similar mode as other nucleoside reverse transcriptase inhibitors, and in addition, it introduces a new hydrogen bond interaction with Trp229. Our novel RTI has high docking scores and the molecular dynamics studies, as well as the analysis of the ligand-receptor interactions in the active site and the ADMET properties suggest advantages and specificities for this potential RTI.
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Resti, Lady Ichwana, Herman Mawengkang, and Elly Rosmaini. "Mathematical Model for Vehicle Routing and Scheduling with Forward and Reverse Logistics." Sinkron 8, no. 3 (2023): 1536–43. http://dx.doi.org/10.33395/sinkron.v8i3.12599.

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Companies usually use cross-docking to reduce logistics costs. The product delivery process from suppliers to retailers and vice versa is facilitated by crossdocking facilities. One of important problem in crossdocking is vehicle routes. In this work we discuss about cross-docking problem for vehicle routes which is brought into the form of an integration model. We also present the strategy to handle the forward and reverse logistics. From this strategy we have a NP-hard mathematical model as the result.
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Wang, Yan, Aidong Wang, Jianhua Wang, Xiaoran Wu, Yijie Sun, and Yan Wu. "Me-Better Drug Design Based on Nevirapine and Mechanism of Molecular Interactions with Y188C Mutant HIV-1 Reverse Transcriptase." Molecules 27, no. 21 (2022): 7348. http://dx.doi.org/10.3390/molecules27217348.

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In this paper, the Y188C mutant HIV-1 reverse transcriptase (Y188CM-RT) target protein was constructed by homology modeling, and new ligands based on nevirapine (NVP) skeleton were designed by means of fragment growth. The binding activity of new ligands to Y188CM-RT was evaluated by structural analysis, ADMET prediction, molecular docking, energy calculation and molecular dynamics. Results show that 10 new ligands had good absorbability, and their binding energies to Y188CM-RT were significantly higher than those of wild-type HIV-1 reverse transcriptase(wt). The binding mode explained that fragment growth contributed to larger ligands, leading to improved suitability at the docking pocket. In the way of fragment growth, the larger side chain with extensive contact at terminal is obviously better than substituted benzene ring. The enhancement of docking activity is mainly due to the new fragments such as alkyl chains and rings with amino groups at NVP terminal, resulting in a large increase in hydrophobic bonding and the new addition of hydrogen bonding or salt bonding. This study is expected to provide reference for the research on non-nucleoside reverse transcriptase inhibitors resistance and AIDS treatment.
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Byler, Kendall, and William Setzer. "Protein Targets of Frankincense: A Reverse Docking Analysis of Terpenoids from Boswellia Oleo-Gum Resins." Medicines 5, no. 3 (2018): 96. http://dx.doi.org/10.3390/medicines5030096.

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Background: Frankincense, the oleo-gum resin of Boswellia trees, has been used in traditional medicine since ancient times. Frankincense has been used to treat wounds and skin infections, inflammatory diseases, dementia, and various other conditions. However, in many cases, the biomolecular targets for frankincense components are not well established. Methods: In this work, we have carried out a reverse docking study of Boswellia diterpenoids and triterpenoids with a library of 16034 potential druggable target proteins. Results: Boswellia diterpenoids showed selective docking to acetylcholinesterase, several bacterial target proteins, and HIV-1 reverse transcriptase. Boswellia triterpenoids targeted the cancer-relevant proteins (poly(ADP-ribose) polymerase-1, tankyrase, and folate receptor β), inflammation-relevant proteins (phospholipase A2, epoxide hydrolase, and fibroblast collagenase), and the diabetes target 11β-hydroxysteroid dehydrogenase. Conclusions: The preferential docking of Boswellia terpenoids is consistent with the traditional uses and the established biological activities of frankincense.
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Ruswanto, Ruswanto, Richa Mardianingrum, Siswandono Siswandono, and Dini Kesuma. "Reverse Docking, Molecular Docking, Absorption, Distribution, and Toxicity Prediction of Artemisinin as an Anti-diabetic Candidate." Molekul 15, no. 2 (2020): 88. http://dx.doi.org/10.20884/1.jm.2020.15.2.579.

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Aldose reductase is an enzyme that catalyzes one of the steps in the sorbitol (polyol) pathway that is responsible for fructose formation from glucose. In diabetes, aldose reductase activity increases as the glucose concentration increases. The purpose of this research was to identify and develop the use of artemisinin as an anti-diabetic candidate through in silico studies, including reverse docking, receptor analysis, molecular docking, drug scan, absorption, and distributions and toxicity prediction of artemisinin. Based on the results, we conclude that artemisinin can be used as an anti-diabetic candidate through inhibition of aldose reductase
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Riza, Hafrizal, Andhi Fahrurroji, Arif Wicaksono, Ahmad Kharis Nugroho, and Sudibyo Martono. "DOCKING STUDY OF METHYL HESPERIDIN AS NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 3 (2018): 85. http://dx.doi.org/10.22159/ijpps.2018v10i3.22724.

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Objective: This study aims to analyze the methyl hesperidin physicochemical properties related to solubility and permeability, and the affinity of methyl hesperidin against reverse transcriptase HIV-1 activity as a competitive substrate.Methods: This research was conducted using the computerized method, ChemOffice 15.0, to predict ligand physicochemical properties related to solubility and permeability, and Autodock Vina with Autodock Tools program to analyze ligand-receptor affinity.Results: The analysis result of physicochemical properties of hesperidin and methyl hesperidin is respectively 300,27 g/Mol, 1,78, and 314,29 g/Mol, 2,04. The docking result shows that the binding energy of hesperidin, methyl hesperidin and zidovudine with receptor are respectively-8,0,-8,8 and-9,3 kcal/Mol. The type of interactions between receptor and hesperidin is van der Waals and phi-phi staked, methyl hesperidin are van der Waals, hydrogen bond, phi-sigma, and phi-phi stacked, and zidovudine is an attractive charge, hydrogen bond, and phi-sigma.Conclusion: Methyl hesperidin has good solubility and permeability, and has affinity with the receptor, a substrate of reverse transcriptase HIV-1.
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Dissertations / Theses on the topic "Reverse docking"

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Bologna, Fabio <1992&gt. "Development of reverse docking protocols for virtual screening in nanomedicine." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amsdottorato.unibo.it/9932/1/bologna_fabio_tesi.pdf.

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One of the first computational chemistry tools that have been used in pharmaceutical research is molecular docking, which infers the interaction between two molecules, usually a small active compound and a receptor, on the basis of their 3D structures. During my three years of PhD studies I worked mainly on re-purposing molecular docking tools to investigate the interactions between a single molecule of interest and a collection of proteins of pharmacological interest. Since this process is essentially the inverse of what is usually done in pharmaceutical research, the technique is called reverse screening. Reverse screening can help in the identification of new therapeutical targets, in predicting toxicological effects and unwanted interactions or in the design of new therapeutic platforms based on the conjugation between a synthetic compound and a protein carrier. In this work, reverse screening has been applied to porphine and phthalocyanine, two chemically related photosensitizers employed in photodynamic therapy, and Gd@C82, the most promising endohedral gadofullerene for theranostic applications. For each of these two types of molecule, a reverse docking protocols has been designed and has allowed the discovery of new potential pharmaceutical targets and carrier systems that can help overcome the physico-chemical limitations to their widespread usage in nanomedicine. Finally, the application of reverse screening protocols to study the interactions between small nanoparticles (d < 5 nm) and 2D materials against bio-molecules was explored. Although theoretically possible, the sheer number of atoms that must be considered and the nanoparticle size result in a plethora of problems since docking tools have been designed with small active molecules in mind. Nevertheless, a new protocol has been devised to perform reverse screening of gold, silver and silica nanoparticles and 2D materials and it has been successfully tested on a small number of proteins.
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COLUCCIA, Antonio. "Indolyl Aryl Sulfones, HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors: Docking and 3-D QSAR studies." Doctoral thesis, La Sapienza, 2008. http://hdl.handle.net/11573/917519.

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Nervall, Martin. "Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8338.

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Cordonnier, Julien. "Toxoplasma gondii : identification par docking inverse sur des cibles moléculaires de composés actifs issus de ressources naturelles." Electronic Thesis or Diss., Reims, 2024. http://www.theses.fr/2024REIMS001.

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Les écorces d’arbres, co-produit de la sylviculture, constituent une source abondante et durable de substances naturelles. Toxoplasma gondii est le parasite responsable de la toxoplasmose, présentant une menace chez les fœtus, les nouveau-nés et les personnes immunodéprimées. Les thérapies actuelles, limitées et mal tolérées, font désormais face à des phénomènes de chimiorésistance. Ce travail de thèse a pour but d’explorer l’espace chimique associé aux écorces d’essences champardennaises, et les cibles protéiques essentielles à T. gondii. Une première évaluation in silico par docking inverse (AMIDEv2.0) a été réalisée afin d’identifier la cible biologique de triterpènes dérivés de la bétulone, isolés de l’Aulne glutineux ayant montré une activité anti-toxoplasmose in vitro. La CDPK3 a été identifiée comme étant la cible la plus probable parmi 87 protéines de T. gondii. Puis, une protéothèque de 25 structures protéiques 3D essentielles à la survie du parasite, 19 ayant été modélisées par homologie, a été constituée. Les composés de la Chimiothèque Nationale Essentielle ont été évalués ensuite sur cette protéothèque en utilisant AMIDEv2.0. Deux protéines ont été identifiées comme de potentielles cibles, dont ATG3, une structure reconstruite à partir d'homologues avec un pourcentage d'identité inférieur à 50%. Deuxièmement, les écorces du Mélèze d'Europe, dont l’extrait n-heptane avait démontré une activité significative (58 % d’inhibition de croissance parasitaire à 100 µg/ml), ont été soumises à un profilage chimique impliquant un fractionnement par Chromatographie de Partage Centrifuge et de déréplication combinant les données issues de la résonance magnétique nucléaire et de la spectrométrie de masse. Les outils VersaDB et CATHEDRAL ont été développés pour faciliter la création de bases de données modulables et l’évaluation du niveau de confiance des annotations. 52 molécules ont ainsi pu être annotées et associées à un score de confiance. En parallèle, des tests in vitro ont démontré que 2 des 12 fractions CPC, majoritairement composées de terpènes, inhibaient à plus de 40% la survie du parasite à 25 µg/ml. Les composés annotés chez L. decidua ont été soumis à AMIDEv2.0. Le croisement des résultats in vitro et in silico, reposant sur le calcul d'un score d'activité biologique, a mis en évidence l'acide 7-oxo-déhydroabiétique et l'acide daniellique, fortement corrélés à l'activité inhibitrice in vitro des écorces. La CDPK1 et la protéine SET containing Protein ont été identifiées comme leurs cibles protéiques probables, fournissant ainsi de premières informations sur leurs mécanismes d'action. Ces deux hits font actuellement l’objet d’une évaluation in vitro afin d’attester l’efficacité de la démarche développée au cours de ces travaux de thèse<br>Tree barks, by-product of forestry industry, constitute an abundant and sustainable source of natural compounds. Toxoplasma gondii is the parasite responsible for toxoplasmosis, posing a threat to fetuses, newborns, and immunocompromised individuals. The current therapeutics, limited and poorly tolerated, are now confronted to chemoresistant phenomena. This doctoral project aims to explore the chemical space associated with tree barks from the Champagne-Ardenne region, as relevant protein targets to fight T. gondii. An initial in silico evaluation using reverse docking (AMIDEv2.0) was carried out to identify biological target for triterpenes derived from betulone, isolated from the European alder, which had exhibited in vitro anti-toxoplasmosis activity. Among 87 proteins of T. gondii, CDPK3 was identified as the most probable target. Subsequently, a bank of 25 essential 3D protein structures for parasite survival, including 19 homology-modeled structures, was compiled. Thereafter, compounds from the Essential National Chemical Library were screened against this protein bank, using AMIDEv2.0. Two proteins were identified as potential targets; one of them was ATG3, a protein structure modeled from homologs with less than 50% identity. Subsequently, the barks of European Larch, whose n-heptane extract had shown significant activity (58% inhibition of parasitic growth at 100 µg/ml), were subjected to a chemical profiling. First, through a fractionation process using Centrifugal Partition Chromatography, and then a dereplication approach combining data from nuclear magnetic resonance and mass spectrometry. Tools like VersaDB and CATHEDRAL were developed to facilitate the creation of custom-databases and assess the confidence level of annotations. 52 molecules were annotated and associated with a confidence score. Simultaneously, in vitro tests demonstrated that 2 out of the 12 CPC fractions, primarily composed of terpenic derivatives, inhibited the parasite's survival by more than 40% at 25 µg/ml. Ultimately, the annotated compounds from L. decidua were subjected to AMIDEv2.0. The overlap between in vitro and in silico results highlighted 7-oxo-dehydroabietic acid and daniellic acid, strongly correlated with the in vitro inhibitory activity of the barks. CDPK1 and the SET-containing Protein are likely protein targets for these two ligands, thereby providing initial insights into their mechanism of action. These two hits are currently undergoing in vitro evaluation to verify the efficiency of developed approach during this doctoral project
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Han, Chia-Jung, and 韓佳榮. "The optimal model of supply chain with reverse logistics under vendor managed inventory and cross-docking." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/09882127951008827449.

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碩士<br>中原大學<br>工業與系統工程研究所<br>100<br>To reduce the waste of resources, the concept of reusing return products in the market has been employed, and such reverse logistics activities have been extended to supply chain system. However, using the reverse logistics activities need to consider both return products and remanufactured products, that makes supply chain management become complex and uncertain. Therefore, this study used the coordination mechanism of Vendor Managed Inventory (VMI) which can coordinate supply chain and reduce bullwhip effect to decrease the loss caused by reverse logistics. Furthermore, this study added the distribution strategy of cross-docking which is better than direct shipment and traditional warehousing. Then, the information requirement in cross-docking can be satisfied through information sharing under VMI. In this study, adding cross-docking in the supply chain with reverse logistics, then using the characteristic of VMI to construct the optimal model of supply chain. The objective of this study is to derive the optimal acquisition price of used product and the optimal order quantity to get the minimal cost of whole supply chain, then performing sensitivity analysis and hypothesis test for parameters. According to the results, retailers and distribution center achieve lower inventory cost, and vendor can reduce the cost through adjusting significant factors of remanufacturing costs for returned product and production costs for new product. Thus related industries could use the model and information in this study to make profitable decisions and achieve the objective for minimal cost of whole supply chain.
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Chao, Ken-Han, and 趙根漢. "The Simulation Design and Analysis of the Integrated Cross-Docking in Forward and Reverse Logistics: Using the Urban Consolidation Centre as an Example." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/z2q3gn.

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碩士<br>國立中興大學<br>企業管理學系所<br>101<br>The study tries to set an Urban Consolidation Centre in the suburban area that combines forward logistics and reverse logistics by cross-docking, which helps firms take their Extended Producer Responsibility（EPR）while increasing the efficiency in logistics system. We figure out some cross-docking facilities and strategies, and then compare the strategies’ performances by system simulation; we also test the effects of arrival rates of trucks, loads in trucks, and the process orders of loads on performances. The results show that in forward logistics, the strategies with pooled doors have better performances in terms of the arrival rates of trucks, while the strategies without pooled doors have better performances in terms of the loads in trucks. In reverse logistics, although changing the load processing orders can improve the performances of the strategies without pooled doors, but there’s no effect on the performances of the strategies with pooled doors. Even so, the strategies with pooled doors are still outstanding. We suggest that future studies can propose more scheduling strategies and use real data to obtain the parameters such that the simulation results become more complete.
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Tambani, Tshifhiwa. "Overexpression and structure-function characterization of HIV-1 Subtype C. reverse transcriptase and protease." Thesis, 2019. http://hdl.handle.net/11602/1423.

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PhD (Microbiology)<br>Department of Microbiology<br>High genetic diversity is a major contributory factor in the development of drug resistance, in addition to challenges in diagnosis and treatment monitoring in the therapeutics of human immunodeficiency virus (HIV) .Within the wide HIV-1 diversity, differences in mutational frequency, disease progression, drug response and transmission amongst HIV-1 subtypes have been shown. In spite HIV-1 subtype C (HIV-1C) being the most prevalent variant globally, none of the available drugs nor screening assays for inhibitory molecules have been developed targeting the genetics of this important subtype. This study therefore aimed to overexpress and biophysically characterize HIV-1C reverse transcriptase and protease to serve as reagents in the development of assays for routine screening of molecules inhibitory to HIV-1C. Heterologous expression of HIV-1C reverse transcriptase and protease isolates that are prevalent in South Africa was carried out in Escherichia coli (E. coli (BL21-DE3). The secondary and tertiary structures of the proteins were determined using, circular dichroism (CD) and fluorescence spectroscopy respectively. Thereafter, interaction studies to delineate interaction properties of natural products for possible inhibition of protease were conducted. Furthermore, in silico studies to determine binding interactions, further confirmed by in vitro binding assays of a pepsin inhibitor homolog (Bm-33) from Brugia malayi , against protease were also conducted. Expressed reverse transcriptase and protease from the globally prevalent HIV-1C were shown to be structurally and functionally intact for application in downstream HIV-1 inhibition assays. Interaction studies on the other hand revealed successful inhibition of the expressed HIV-1C PR with gallotanin. Furthermore, binding interactions of Bm-33 and HIV-1 PR revealed the first intermolecular interactions of the two molecules displaying possible inhibition of HIV-1 PR<br>NRF
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Book chapters on the topic "Reverse docking"

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Ruiz-Moreno, Angel Jonathan, Alexander Dömling, and Marco Antonio Velasco-Velázquez. "Reverse Docking for the Identification of Molecular Targets of Anticancer Compounds." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0759-6_4.

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Gunawan, Aldy, Audrey Tedja Widjaja, Pieter Vansteenwegen, and Vincent F. Yu. "Vehicle Routing Problem with Reverse Cross-Docking: An Adaptive Large Neighborhood Search Algorithm." In Lecture Notes in Computer Science. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-59747-4_11.

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Unissa, Ameeruddin Nusrath, and Luke Elizabeth Hanna. "Computational Analysis of Reverse Transcriptase Resistance to Inhibitors in HIV-1." In Big Data Analytics in HIV/AIDS Research. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-3203-3.ch001.

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Reverse transcriptase (RT) is a vital enzyme in the process of transcription of HIV-1. The nucleoside analogues of RT inhibitors (NRTIs) act by substrate competition and chain termination as they resemble a nucleotide. To understand the basis of RT resistance in HIV-1, in this chapter, one of the clinically essential mutants Q151M of RT which exhibits multi-resistance to many NRTIs was modeled and docked with NRTIs in comparison to wild type (WT). The results of docking indicate that the WT showed high affinity with all inhibitors compared to the mutant (MT). It can be suggested that the high affinity in WT could be attributed to the favorable interactions with all inhibitors that lacks in MT due to amino acid substitution that leads to structural changes in MT protein, which alters the favorable network of interaction and eventually imparts resistance to all inhibitors.
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"Docking-Based Scoring Parameters Based QSAR Modeling on a Dataset of Bisphenylbenzimidazole as Non-Nucleoside Reverse Transcriptase Inhibitor." In Chemometrics Applications and Research. Apple Academic Press, 2016. http://dx.doi.org/10.1201/b19853-18.

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Molina-Gallardo, Axel R., Yesica R. Cruz-Martínez, Julieta Orozco-Martínez, Israel Valencia Quiroz, and C. Tzasna Hernández-Delgado. "The Roles of Farnesol and Farnesene in Curtailing Antibiotic Resistance." In Biotechnology and Drug Development for Targeting Human Diseases. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815223163124090005.

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In the extensive domain of “biotechnology and drug development for targeting human diseases”, essential oils have long been revered for their therapeutic potential. Among these, farnesol and farnesene stand out due to their pharmacological attributes. As the challenge of antibiotic resistance intensifies, the scientific community is increasingly exploring the potential of these traditional remedies. Using the KirbyBauer agar diffusion method, a qualitative assessment was conducted on two grampositive and two gram-negative bacterial strains. The broth microdilution technique further determined the Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC), and the sensitizing impacts of these compounds. Both farnesol and farnesene exhibited antibacterial efficacy against all evaluated strains. Their synergistic potential was highlighted when combined with clavulanic acid, cefuroxime, and cefepime. Among these combinations, farnesene paired with cefepime showed pronounced efficacy against Escherichia coli 82 MR, with an MIC of 0.47 μg/mL. In contrast, in the investigation of Staphylococcus aureus 23MR, it was observed that this particular strain exhibited an increased sensitivity when exposed to combinations containing farnesol. Notably, the Minimum Inhibitory Concentration (MIC) was determined to be 0.03 µg/mL in the presence of both antibiotic agents. To gain deeper molecular insights, docking experiments were performed with the βlactamases of E. coli and S. aureus, focusing on the most effective combinations. All tested compounds—cefuroxime, cefepime, farnesene, and farnesol—acted as noncompetitive inhibitors, suggesting their potential mechanisms of action.
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Conference papers on the topic "Reverse docking"

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Ji, Yeye. "Application of reverse docking in traditional Chinese medicine research." In International Conference on Biological Engineering and Medical Science (ICBIOMed2022), edited by Gary Royle and Steven M. Lipkin. SPIE, 2023. http://dx.doi.org/10.1117/12.2669488.

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Alargić, Aleksa P., Bojan D. Levovnik, and Miloš M. Svirčev. "Workflow automation of high-throughput inverse docking using Pharmmapper." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.678a.

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In this paper, we present a novel, modular script Pharmmapper-Mass-Docker for the inverse docking workflow automation based on the pharmacophore screening results obtained on the Pharmmapper server. Pharmmapper-Mass-Docker streamlines download, manipulation, and entire inverse docking of the Pharmmapper results, encompassing essential steps like ligand/gridbox/binding site coordinate extraction (via centroid generation) and obtaining the output data ready for further comprehensive data analysis. By automating the entire inverse docking procedure, our modular script potentially enhances data management efficiency during inverse docking and reverse screening, empowering the researchers to efficiently discover and explore novel protein-ligand interactions.
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Gunawan, Aldy, Audrey Tedja Widjaja, Pieter Vansteenwegen, and Vincent F. Yu. "Vehicle Routing Problem with Forward and Reverse Cross-Docking: Formulation and Matheuristic Approach." In 2021 IEEE 17th International Conference on Automation Science and Engineering (CASE). IEEE, 2021. http://dx.doi.org/10.1109/case49439.2021.9551486.

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Monteiro, Alex, Marcus Scotti, and Luciana Scotti. "MOLECULAR DOCKING OF FRUCTOSE-DERIVED NUCLEOSIDE ANALOGS AGAINST REVERSE TRANSCRIPTASE OF HIV-1." In MOL2NET 2019, International Conference on Multidisciplinary Sciences, 5th edition. MDPI, 2019. http://dx.doi.org/10.3390/mol2net-05-06178.

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Ye, Li, Shuangxi Gu, Cheng Qian, and Xiulian Ju. "3D-QASR and molecular docking study of diarylpyrimidines as HIV-1 reverse transcriptase." In International conference on Human Health and Medical Engineering. WIT Press, 2014. http://dx.doi.org/10.2495/hhme131032.

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Zhang, Zhihong. "Value Study on the Application of Cross Docking Strategy in Recall Reverse Logistics." In International Academic Workshop on Social Science (IAW-SC-13). Atlantis Press, 2013. http://dx.doi.org/10.2991/iaw-sc.2013.30.

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Widjaja, Audrey Tedja, Aldy Gunawan, Panca Jodiawan, and Vincent F. Yu. "Incorporating a Reverse Logistics Scheme in a Vehicle Routing Problem with Cross-Docking Network: A Modelling Approach." In 2020 IEEE 7th International Conference on Industrial Engineering and Applications (ICIEA). IEEE, 2020. http://dx.doi.org/10.1109/iciea49774.2020.9101972.

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Monteiro, Alex, Isadora Luna, Marcus Scotti, and Luciana Scotti. "In silico analysis of cytotoxicity, rate of absorption and molecular docking of natural products against protease, integrase and HIV-1 reverse transcriptase." In MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition. MDPI, 2018. http://dx.doi.org/10.3390/mol2net-04-05539.

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Renault, J.-H., P. Darme, J. Cordonnier, et al. "Short Lecture “Combination of high-throughput reversed docking and 13C NMR-based chemical profiling for new antimicrobial compounds and potential biological target identification”." In GA – 70th Annual Meeting 2022. Georg Thieme Verlag KG, 2022. http://dx.doi.org/10.1055/s-0042-1758981.

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RUIZ AGUILAR, JUAN JESÚS, IGNACIO J. TURIAS, MAR CERBÁN, MARÍA JOSÉ GONZÁLEZ, and ÁNGEL PULIDO. "Time analysis of the containerized cargo flow in the logistic chain using simulation tools: the case of the Port of Seville (Spain)." In CIT2016. Congreso de Ingeniería del Transporte. Universitat Politècnica València, 2016. http://dx.doi.org/10.4995/cit2016.2016.3083.

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Abstract:
The logistic chain that connects the capital of Spain (Madrid) with the Canary Islands has the Port of Seville as the port node. This port node makes possible to switch from one transport mode (railway) to another (maritime) at the container terminal of the port. Some constraints, such as the operational time window that restricts the freight train access into the port in a certain time-slot or the need of the reversal of the train before entering into port, lead to generate important time delays in the intermodal chain. A time analysis of the process is necessary in order to check the critical points. A simulation of the whole process from the goods departing the origin station by train until they leave the port of Seville by ship to the Canary Islands is performed. To this aim, a queuing model network was developed in order to simulate the travel time of the cargo. The database is composed of daily departures of goods train and daily departures of vessels (including times of docking, berthing or load/unload cargo). The final objective of this work is twofold: firstly, to provide a validated model of the containerized cargo flow and secondly, to demonstrate that this kind of queuing models can become a powerful supporting tool in making decisions about future investments.DOI: http://dx.doi.org/10.4995/CIT2016.2016.3083
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