Relevant bibliographies by topics / Molecular Docking Simulation Druglikeness Screening

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  2. Dissertations / Theses
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Academic literature on the topic 'Molecular Docking Simulation Druglikeness Screening'

Author: Grafiati
Published: 4 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "Molecular Docking Simulation Druglikeness Screening"

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Thuy, Bui Thi Phuong, Vo Duy Nhan, Nguyen Minh Quang, Nguyen Thanh Duoc, and Pham Van Tat. "Evaluation of SARS‐CoV‐2 inhibition of some compounds inCYMBOPOGON CITRATUS oil combining docking and molecular dynamics simulations." Vietnam Journal of Chemistry 59, no. 6 (2021): 790–99. http://dx.doi.org/10.1002/vjch.202100022.

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AbstractThe visual screening and simulation methods were used to evaluate the inhibitory ability of 34 compounds in Cymbopogon citratus oil against SARS‐CoV‐2. We chose the best compound, SC22, with a DS of ‐12.80 Kcal. mol‐1 with a distance RMSD of 0.23. This was the most effective compound at inhibiting the viral protein 6LU7. For the protein ACE2 or an endemic host receptor, the docking ability of SC22 showed DS = ‐13.13 Kcal.mol‐1 and RMSD = 1.32 Å; SC10 docked in DS = ‐12.79 Kcal.mol‐1 and RMSD = 0.91 Å; SC11 gave the docking values DS = ‐12.77 Kcal.mol‐1 and RMSD = 1.15 Å. SC26 showed DS
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Ajala, Olusegun Samson, Moshood Olusola Akinleye, Mbang Owolabi, and Grace Ukpo. "In Silico Evaluation of Aromatase Inhibitory Anti-benign Prostatic Hyperplasia Potentials of Spirostan Sapogenins." Malaysian Journal of Pharmaceutical Sciences 21, no. 1 (2023): 63–89. http://dx.doi.org/10.21315/mjps2023.21.1.5.

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Inherent oestrogen receptor alpha (ERα) and other nuclear receptor signaling activities of typical aromatase inhibitors (AIs) preclude their clinical use as anti-oestrogenic anti-benign prostatic hyperplasia (anti-BPH) agents. Spirostan sapogenins (SS) constitute a chemical space from which AIs without such deterrents could be sought. This work was aimed at in silico discovery of clinical aromatase inhibitory anti-oestrogenic anti-BPH drug leads. Fortysix SS were docked against an inhibitor conformation of the human placenta aromatase. Nuclear receptor signaling activation tendencies of seven
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Alkaff, Ahmad Husein, Mutiara Saragih, Shabrina Noor Imana, Mochammad Arfin Fardiansyah Nasution, and Usman Sumo Friend Tambunan. "Identification of DNA Methyltransferase-1 Inhibitor for Breast Cancer Therapy through Computational Fragment-Based Drug Design." Molecules 26, no. 2 (2021): 375. http://dx.doi.org/10.3390/molecules26020375.

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Epimutation by DNA Methyltransferase 1 (DNMT1), an epigenetic regulator enzyme, may lead to the proliferation of breast cancer. In this report, 168,686 natural products from the PubChem database were screened and modified by in silico method to acquire the potential inhibitor of DNMT1. The initial screening of PubChem natural products using Lipinski’s and Veber’s rules of three and toxic properties have resulted in 2601 fragment candidates. Four fragments from pharmacophore-based molecular docking simulation were modified by utilizing FragFP and the Lipinski’s and Veber’s rules of five, and re
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Ariavianti, Elsafira, Filia Stephanie, and Usman Sumo Friend Tambunan. "Virtual Screening Based on Pharmacophore to Discover Host ER Alpha-Glucosidase II Inhibitor for Dengue Therapy." Key Engineering Materials 840 (April 2020): 221–29. http://dx.doi.org/10.4028/www.scientific.net/kem.840.221.

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Dengue is one of the crucial diseases in human-caused by dengue virus (DENV) infection. However, the development of DENV antiviral is often facing a problem because no effective drug to treat infection caused by all DENV serotypes. The inhibition of host protein involved in DENV life cycle can be a potential approach in dengue drug discovery, and also avoiding antiviral resistance. Endoplasmic Reticulum (ER) α-glucosidase II is one of the target host protein in DENV endoplasmic reticulum that plays an important role in the maturation process of DENV envelope glycoprotein. Natural products have
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Kharisma, Viol Dhea, Santika Lusia Utami, Wahyu Choirur Rizky, et al. "Molecular docking study of Zingiber officinale Roscoe compounds as a mumps virus nucleoprotein inhibitor." Dental Journal (Majalah Kedokteran Gigi) 56, no. 1 (2023): 23–29. http://dx.doi.org/10.20473/j.djmkg.v56.i1.p23-29.

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Background: Mumps virus (MuV) can trigger severe infections, such as parotitis, epididymo-orchitis, and meningitis. The effectiveness of MuV vaccine administration has been proven, but current outbreaks warrant the development of antivirals against MuV. Zingiber officinale var. Roscoe or ginger is often used as an alternative remedy. Currently, there are no known in vitro or in vivo studies that investigate ginger as an MuV antiviral. Purpose: This study aims to evaluate the antiviral potency of the bioactive compounds in Zingiber officinale var. Roscoe against MuV. Methods: Antiviral activity
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Ibrahim, Mutiat B., Adeola T. Kola-Mustapha, Niyi S. Adelakun, and Neil A. Koorbanally. "Phytoconstituents from Markhamia tomentosa Bind To HPV Oncoprotein with Apoptogenic Potential: A Molecular Modeling Approach." Annals of Science and Technology 6, no. 2 (2021): 28–46. http://dx.doi.org/10.2478/ast-2021-0008.

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Abstract Markhamia tomentosa crude extract and fractions exhibited potent growth inhibitory effects capable to induce apoptosis in cervical (HeLa) cancer cell line via in vitro model. Presently, interaction of M. tomentosa phytoconstituents with molecular drug targets to exert its anticancer property is evaluated via in silico study. Identified phytoconstituents from M. tomentosa were retrieved from PubChem database and docked in active sites of HPV 16 E6, caspase -3 and caspase -8 targets using AutoDockVina from PyRx software. Screening for druglikeness; and absorption, distribution, metaboli
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Azmi, Muhammad Bilal, Simran Kumari, Sakina Aquil, et al. "KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through in silico analysis." PLOS One 20, no. 6 (2025): e0324678. https://doi.org/10.1371/journal.pone.0324678.

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Propolis, a resinous compound produced by bees, possesses diverse medicinal properties and has gained significant attention for its potential in cancer therapy. This study investigated the therapeutic significance of propolis-derived compounds targeting the kinesin-like protein KIFC1, a motor protein overexpressed in various cancers, using a multistep computational methodology. Therefore, it is essential to utilize different in silico methods to predict their therapeutic potential. A 3D library of propolis-derived compounds sourced from previously published literature was compiled and screened
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Nasution, Rani Sakila, Indang Dewata, Nofri Yuhelman, Neny Sandrawati та Arif Juliari Kusnanda. "Molecular Docking and Pharmacoinformatics Study of Bioactive Compounds in Sweet Flag (Acorus calamus L.) as Antidiabetic Agents Targeting α-Glucosidase". Jurnal Pijar Mipa 20, № 4 (2025): 598–604. https://doi.org/10.29303/jpm.v20i4.8994.

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Diabetes mellitus (DM) is a chronic metabolic disorder whose prevalence continues to rise, necessitating safer and more effective therapeutic alternatives. This study aims to explore the potential of active compounds from the calamus plant (Acorus calamus L.) as candidates for α-glucosidase enzyme inhibitors using an in silico approach. Pharmacokinetic screening, toxicity prediction, and Lipinski's Rule of Five screening were conducted to assess the pharmacological suitability of the compounds, followed by molecular docking using MOE 2022 software. The results of the study showed that several
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Bepari, Asim Kumar, and Hasan Mahmud Reza. "Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation." PeerJ 9 (April 13, 2021): e11261. http://dx.doi.org/10.7717/peerj.11261.

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Background The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has ravaged lives across the globe since December 2019, and new cases are still on the rise. Peoples’ ongoing sufferings trigger scientists to develop safe and effective remedies to treat this deadly viral disease. While repurposing the existing FDA-approved drugs remains in the front line, exploring drug candidates from synthetic and natural compounds is also a viable alternative. This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime mol
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Ogunyemi, Oludare M., Gideon A. Gyebi, Abdo A. Elfiky, et al. "Alkaloids and flavonoids from African phytochemicals as potential inhibitors of SARS-Cov-2 RNA-dependent RNA polymerase: an in silico perspective." Antiviral Chemistry and Chemotherapy 28 (January 2020): 204020662098407. http://dx.doi.org/10.1177/2040206620984076.

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Corona Virus Disease 2019 (COVID-19) is a pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Exploiting the potentials of phytocompounds is an integral component of the international response to this pandemic. In this study, a virtual screening through molecular docking analysis was used to screen a total of 226 bioactive compounds from African herbs and medicinal plants for direct interactions with SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). From these, 36 phytocompounds with binding affinities higher than the approved reference drugs (remdesivir and sobosivi
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Dissertations / Theses on the topic "Molecular Docking Simulation Druglikeness Screening"

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Rieux, Charlotte. "Etude des ADN glycosylases de la superfamille structurale Fpg/Nei par modélisation moléculaire, de nouvelles cibles thérapeutiques potentielles dans les stratégies anti-cancer." Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2023/document.

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L’ADN, support de l’information génétique, est constamment altéré par des agents physiques ou chimiques d’origines endogènes (métabolisme) et exogènes (UV, radiations ionisantes, produits chimiques) dont les effets sont génotoxiques. Ces modifications structurales délétères de l’ADN sont éliminées par de nombreux mécanismes de réparation. Parmi eux, le système de réparation par excision de bases (BER) est initié par les ADN glycosylases qui reconnaissent et éliminent les bases endommagées. Dans certaines stratégies anti-cancéreuses, l’utilisation de la chimiothérapie et la radiothérapie ont po
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Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.

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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-an
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Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.

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Beck, Guillaume. "Recherche de nouveaux agents thérapeutiques dans le traitement des lymphomes à cellules B." Thesis, La Réunion, 2020. http://www.theses.fr/2020LARE0002.

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Le lymphome à cellule B est un type de cancer qui se développe dans le système lymphatique. Des études réalisées par Meadows et al ont indiqué que PI3Kδ pouvait constituer une cible thérapeutique dans ce cancer. Le but de cette étude est d’identifier des inhibiteurs du site de liaison à l’ATP de la protéine kinase PI3Kδ qui possède une forte affinité. Un criblage virtuel de 350 composés ciblant la protéine PI3Kδ a été réalisé. La validation préalable d’un protocole de scoring a été réalisée préalablement sur notre protéine d’intérêt PI3Kδ. Ce protocole contient différentes étapes de sélection
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Asses, Yasmine. "Conception par modélisation et criblage in silico d'inhibiteurs du récepteur c-Met." Phd thesis, Université Henri Poincaré - Nancy I, 2011. http://tel.archives-ouvertes.fr/tel-00653609.

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L'enjeu des travaux effectués au cours de cette thèse est l'extraction in silico de molécules potentiellement intéressantes dans le processus d'inhibition du récepteur tyrosine kinase c-Met. La faculté de cette protéine à interagir dans les phénomènes d'embryogenèse et de réparation tissulaires rendent son inhibition cruciale dans les traitements contre les développements tumoraux où c-Met se trouve impliquée. Dans ce but, la stratégie que nous avons employée implique l'utilisation de plusieurs méthodes in silico de conception rationnelle de médicaments. Nous avons utilisé comme support les mu
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Book chapters on the topic "Molecular Docking Simulation Druglikeness Screening"

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Mursal, Mohd, Mohammad Ahmad, Sahil Hussain, and Mohemmed Faraz Khan. "Navigating the Computational Seas: A Comprehensive Overview of Molecular Docking Software in Drug Discovery." In Unravelling Molecular Docking - From Theory to Practice [Working Title]. IntechOpen, 2024. http://dx.doi.org/10.5772/intechopen.1004802.

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Molecular docking software is an indispensable tool in the dynamic landscape of computational biology and drug discovery. This software facilitates the simulation and prediction of interactions between small molecules and target proteins, offering a detailed glimpse into molecular binding phenomena. Employing sophisticated algorithms, these programs assess binding affinity, predict binding modes, and contribute crucial insights to streamline drug development processes. Examples of widely used molecular docking software include AutoDock, GOLD, and DOCK, each renowned for their capabilities in o
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Jays, Judy, P. Parasuram, and J. Saravanan. "Screening of Some Novel Isoxazoles Against C. Albicans for their Potential Use as antifungals: A Computational Approach." In Current Trends in Drug Discovery, Development and Delivery (CTD4-2022). Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/9781837671090-00103.

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Antifungal resistance represents a major challenge for treating invasive fungal infections due to the limited arsenal of systemic antifungal agents. Azole resistance among Candida and Aspergillus species and the spread of such species is alarming. Isoxazoles play a significant role in the field of medicinal chemistry. The great interest associated with this class of compounds is their versatility as synthetic intermediates. Isoxazole derivatives were found to possess anti-bacterial, anti-fungal, anti-inflammatory, pesticidal and herbicidal activities. This study focuses on screening some novel
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James, Jithu Jerin, Parasuraman Pavadai, and K. V. Sandhya. "Screening of Placental Proteins Against Proteases for their Potential Use in Osteoarthritis: A Computational Approach." In Current Trends in Drug Discovery, Development and Delivery (CTD4-2022). Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/9781837671090-00057.

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Osteoarthritis is a chronic joint condition owing to increasing articular cartilage weakening and deterioration. Novel agents targeting articular cartilage molecular mechanisms seem to be most promising. The placental tissues are biocompatible, immunoprivileged and rich in bio factors such as growth factors, cytokines, extracellular matrix and proteins. Placental proteins might reduce cartilage degradation through suppressing the expression of matrix metalloproteases. This study focuses on screening placental proteins against proteases using protein-protein docking and dynamic studies. Protein
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Das, Jyotirmoy, Basudev Tassa, and Biplab Kumar Das. "COMPUTER AIDED DRUG DESIGNING – A NOVEL APPROACH METHOD." In Futuristic Trends in Agriculture Engineering & Food Sciences Volume 3 Book 8. Iterative International Publisher, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bcag8p6ch2.

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Today, there possesses different types of drugs against different diseases and various sophisticated technologies but still it is not enough to develop drugs instantly against a new emerging disease as drug designing and development is a complex and lengthy process and requires a huge amount of money. In 21st generation, other reliable methodsare being used to speed up the drug discovery process following the combinatorial chemistry emergence, known as computer aided drug designing where drugs leads are being predicted among the huge number of molecules by checking the interaction between the
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Yim Wen-wai, Chien Shu, Kusumoto Yasuyuki, Date Susumu, and Haga Jason. "Grid Heterogeneity in In-silico Experiments: An Exploration of Drug Screening Using DOCK on Cloud Environments." In Studies in Health Technology and Informatics. IOS Press, 2010. https://doi.org/10.3233/978-1-60750-583-9-181.

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Large-scale in-silico screening is a necessary part of drug discovery and Grid computing is one answer to this demand. A disadvantage of using Grid computing is the heterogeneous computational environments characteristic of a Grid. In our study, we have found that for the molecular docking simulation program DOCK, different clusters within a Grid organization can yield inconsistent results. Because DOCK in-silico virtual screening (VS) is currently used to help select chemical compounds to test with in-vitro experiments, such differences have little effect on the validity of using virtual scre
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Conference papers on the topic "Molecular Docking Simulation Druglikeness Screening"

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Gosoi, Dipshikha, Ratul Saikia, Jatin Kalita та ін. "Combining Virtual Screening, Molecular Docking and Simulation studies towards the discovery of β-secretase (BACE) inhibitors". У 2018 International Conference on Bioinformatics and Systems Biology (BSB). IEEE, 2018. http://dx.doi.org/10.1109/bsb.2018.8770645.

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Lokwani, Deepak K., Sangita R. Chavan, Aniket P. Sarkate, Prabhu M. Natarajan, Vidhya R. Umapathy, and Shirish P. Jain. "Virtual Screening of Natural Compounds as Potential SARS-CoV-2 Main Protease Inhibitors: A Molecular Docking and Molecular Dynamics Simulation Guided Approach." In ECSOC 2023. MDPI, 2023. http://dx.doi.org/10.3390/ecsoc-27-16049.

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Nasution, M. A. F., F. Stephanie, and U. S. F. Tambunan. "Pharmacophore-based virtual screening and molecular docking simulation of flavonoids as smoothened protein inhibitor of Hedgehog signaling pathways." In PROCEEDINGS OF THE 4TH INTERNATIONAL SYMPOSIUM ON CURRENT PROGRESS IN MATHEMATICS AND SCIENCES (ISCPMS2018). AIP Publishing, 2019. http://dx.doi.org/10.1063/1.5132487.

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Rubani, Muhammad, and Arli Aditya Parikesit. "Molecular Simulation of Coffee Beans’ Natural Products as Lead Compounds for Stroke Remedy." In The 6th International Conference on Science and Engineering. Trans Tech Publications Ltd, 2024. http://dx.doi.org/10.4028/p-k5delo.

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The consumption of coffee has its health benefits and its risks, one of the risks is mostly related to cardiovascular diseases. One of the diseases is hypertension which is considered “the silent killer” as it is a serious condition which promotes other complications and typically has no symptoms for a period of time until it has done significant damage. Acute hypertension can lead to a stroke. It is a very serious medical condition where the blood flow to the brain is poor, causing the death of cells within the brain. Some medications, surgeries and other healthcare programs are capable of co
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Reports on the topic "Molecular Docking Simulation Druglikeness Screening"

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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are
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