- Using docking of suspected ligands, we were able to show Guanine and Adenine diand tri-nucleotides readily bind to the identified site. (scirp.org)
- Molecular docking analysis of designed ligands on VP40 of Ebola Virus. (iium.edu.my)
- We performed molecular docking simulation with six different inhibitors (ligand), which includes DTNB, NSC695265, thionitrobenzoic acid, 2-nitro-5-thiocyanobenzoic acid, 2-nitro-5-sulfo-sulfonyl-benzoic acid and NSC517871 into the redox-active site [C37-G38-H39-C40] of the PDI enzyme and the activity was inferred by redox inhibitory models. (biomedcentral.com)
- Computational quest for finding potential Ebola VP40 inhibitors: a molecular docking study = [pencarian pengiraan untuk mencari potensi perencat Ebola VP40: suatu kajian mengedok molekul]. (iium.edu.my)
- Nearly, 100 ns MD simulation indicated the stability of the designed compounds at 100 ns, while molecular mechanics-Poisson Boltzmann surface area calculation showed that the designed compound had a higher affinity than that of the parent compound. (japsonline.com)
- The stability of interacting residues of proteins with compounds was identified via molecular dynamics and free binding energy calculations using Amber 12. (ui.ac.id)
- Highest occupied molecular orbital and lowest unoccupied molecular orbital were analysed to determine the lead compounds' biological and pharmacological efficacy . (bvsalud.org)
- The docking simulations study revealed that these synthesized compounds displayed hydrogen bonding, electrostatic and hydrophobic interactions with active site residues. (biomedcentral.com)
- The structure activity relationship studies of these compounds were also corroborated with the help of molecular modeling studies. (biomedcentral.com)
- C ) Molecular screening of FDA-approved compounds led to identification of top hits. (elifesciences.org)
- Among the 37 compounds docked, 5 compounds showed good binding affinity and pharmacokinetic properties. (researchsquare.com)
- Molecular docking was performed to evaluate the binding affinity of 97 phenolic compounds (phenolics) with the SARS-CoV-2 S-protein receptor-binding domain (RBD). (elis.sk)
- Molecular dynamics (MD) simulation was carried out to assess the stability of interactions between top-ranked compounds and S-protein RBD. (elis.sk)
- Molecular Docking of Polyphenol Compounds from Anacardium occidentalewith Alpha-Glucosidase and Dipeptidyl-Peptidase-4 Enzymes. (iium.edu.my)
- Molecular Docking and Dynamics Simulation of Natural Phenolic Compounds with GSK-3β: A Putative Target to Combat Mortality in Patients with COVID-19. (cdc.gov)
- Machine learning for yield prediction for chemical reactions using in situ sensors JOURNAL OF MOLECULAR GRAPHICS & MODELLING. (nottingham.ac.uk)
- The present study investigates the effect of curcumin on PMRS activity of erythrocytes isolated from Wistar rats in vitro and in vivo and validated through an in silico docking simulation study using Molegro Virtual Docker (MVD). (hindawi.com)
- We demonstrated that in silico docking experiment can be effectively carried out to recognize the redox inhibitory models of PDI with inhibitor molecules. (biomedcentral.com)
- Human molecular genetics 2023 0 0. (cdc.gov)
- International journal of molecular sciences 2023 0 0. (cdc.gov)
- Molecular dynamic simulations have been done for top most active compound for validating its α-glucosidase and α-amylase inhibitory potential, RMSD analysis of ligand protein complex suggested the stability of top most active compound 5o in binding site of target proteins. (biomedcentral.com)
- All simulations were performed with a common feature: the binding of a potential ligand to Asn inside the bromodomain binding pocket. (enamine.net)
- Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
- Interestingly we found that number of docked clusters with each ligand varies in the range of five to eight and conveys that the binding specificity of each inhibitor varies for PDI. (biomedcentral.com)
- The importance of hydrogen bonding and ringâ ring interactions is explored along with an examination of the major docking arrangements. (sharcnet.ca)
- On the one hand, we reduce biology to its molecular components, and seek to change how these fit together using synthetic molecules we design. (ucsf.edu)
- Journal of Molecular Biology. (lu.se)
- The results revealed that the top hits responded to all of the pharmacological druglikening criteria and had the best interaction residues, fitness scores, and docking scores. (bvsalud.org)
- The interaction of human topoisomerase 1B and dimethylmyricacene, a compound prepared semisynthetically from myricanol extracted from Myrica cerifera root bark, was investigated using enzymatic activity assays and molecular docking procedures. (mdpi.com)
- A Computational Investigation on Chitosan Derivatives using Pharmacophore- based Screening, Molecular Docking, and Molecular Dynamics Simulations against Kaposi Sarcoma. (bvsalud.org)
- Screening and binding kinetics and molecular simulation dynamics runs of drugs against C-terminal helices of Nsp1 (Nsp1-C-ter). (elifesciences.org)
- Analysis of virulence related gene expression and computational simulations of pivotal proteins involved in pathogenesis demonstrate that myricetin downregulates the saeR global regulator and interacts with sortase A and α-hemolysin. (nature.com)
- With further molecular dynamic simulations, these sites are shown to be plausible by conducting simple computational based solubility tests as cross validation. (scirp.org)
- These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos. (nih.gov)
- It is now well-established that from early lesion to vulnerable plaque formation, numerous cellular and molecular inflammatory components participate in the disease process. (researchgate.net)
- This enzyme, which is the unique molecular target of the natural anticancer compound camptothecin, acts by nicking one DNA strand and forming a transient protein-DNA covalent complex. (mdpi.com)
- To develop novel and more potent quinazoline-phosphoramidate mustard conjugates as epidermal growth factor receptor (EGFR) inhibitor, three-dimensional quantitative structure-activity relationship [comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)] combined with molecular docking were performed. (japsonline.com)
- In this study, emodin derivatives were conducted as an inhibitor candidate of capsid assembly by disruption formation dimer-dimer HBV core protein using molecular docking and dynamic simulation. (ui.ac.id)
- In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. (biorxiv.org)
- Homology modeling and docking studies of δ19-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. (iium.edu.my)
- 2013) The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins. (scirp.org)
- Additionally, we run docking calculations for BPTF protein that also contains bromodomain. (enamine.net)
- We used a structure-based approach, molecular docking calculations, as the main method for the library design. (enamine.net)
- Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation. (iium.edu.my)
- Exploration of the Shared Molecular Mechanisms between COVID-19 and Neurodegenerative Diseases through Bioinformatic Analysis. (cdc.gov)
- The top hits were examined using molecular docking , absorption , distribution, metabolism and excretion. (bvsalud.org)
- Methods: Structure-based virtual docking approach was used to design of benzoylated emodin derivatives into HBV core protein as receptor using Molegro Virtual Docker 6.0 program. (ui.ac.id)
- COBRAMM: A Tunable QM/MM Approach to Complex Molecular Architectures. (unibo.it)
- Enables simulations of clinical trials on a virtual population of prostate cancer patients being treated with a gonadotropin GnRH agonist. (insilicotrials.com)
- Cyclacel utilized in-house structure-based drug design approaches to determine the 3D structure of the molecule and conducted molecular docking simulations to determine the optimal binding location. (scienceboard.net)
- Shared molecular signatures between coronavirus infection and neurodegenerative diseases provide targets for broad-spectrum drug development. (cdc.gov)
- The broad range of curcumin's biological properties is due to its ability to bind to over 100 identified different molecular targets [ 17 ]. (hindawi.com)
- Molecular docking and MD simulations were performed utilizing the AutoDock and Discovery Studio Client version, respectively. (elis.sk)
- There is a great need to find molecular biomarkers predicting increased progression risk in GERD-Barrett's metaplasia-dysplasia-adenocarcinoma sequence to improve risk assessment and stratification of patients to surveillance program. (who.int)
- Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. (nih.gov)