Keywords: 15-PGDH; Molecular dynamics simulation; Molecular docking; PGE2; MM-GBSA;
مقالات ISI (ترجمه نشده)
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Keywords: α-CD; alpha-cyclodextrin; AC; antioxidant activity; ABTS; 2,2â²-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid; β-CD; beta-cyclodextrin; DZ; daidzein; EE (%); encapsulation efficiency (%); FE-SEM; field emission scanning electron microscopy; FT-IR;
Keywords: Drug design; Molecular selectivity; Molecular dynamics; MM-GBSA; Coumarin derivatives; MAO;
Keywords: PAMAM dendrimers; Drug delivery; Molecular dynamics; MM-GBSA; MALDI-MS
Keywords: Estrogen receptor; Ligand selectivity; Molecular dynamics simulation; MM-GBSA;
Keywords: Protonation; Quantum mechanics/molecular mechanics; Quantum polarized ligand docking; Histone deacetylase inhibitors; Binding free energies; MM-GBSA;
Keywords: Sirtuin; MM-GBSA; MM-PBSA; Virtual screening
A Computational workflow for the identification of the potent inhibitor of type II secretion system traffic ATPase of Pseudomonas aeruginosa
Keywords: kj/mol; kilojoule per mol; MD; molecular dynamics; MM; molecular mechanics; MM-GBSA; molecular mechanics - generalized born and surface area; OPLS; optimized potential for liquid simulations; GBSA; generalized-born surface area; PME; particle mesh ewa
Interactions of 2-phenyl-benzotriazole xenobiotic compounds with human Cytochrome P450-CYP1A1 by means of docking, molecular dynamics simulations and MM-GBSA calculations
Keywords: 2-Phenyl-benzotriazole; Molecular docking; Molecular dynamics simulations; MM-GBSA;
Theoretical study of the intermolecular recognition mechanism between Survivin and substrate based on conserved binding mode analysis
Keywords: Survivin; Recognition mechanism; Protein-protein interaction; MD simulations; MM-GBSA; Drug design;
Synthesis and biological evaluation of a library of hybrid derivatives as inhibitors of influenza virus PA-PB1 interaction
Keywords: Anti-Influenza; PA-PB1; RdRp; Amino acid coupling; SPPS; Diphenyl-pyridine; AcOEt; Ethyl acetate; CC50; Half maximal cytotoxic concentration; cRNA; complementar RNA; DCM; dichloromethane; DDQ; 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone; DIPEA; N,N-Diisopro
Experimental and theoretical studies on tautomeric structures of a newly synthesized 2,2â²(hydrazine-1,2-diylidenebis(propan-1-yl-1-ylidene))diphenol
Keywords: Schiff base, tautomeric forms; AIM; Molecular docking; MM-GBSA;
Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors
Keywords: CREBBP; Bromodomain; Molecular dynamics; Propionylshikonin; MM-PBSA; MM-GBSA; QM/MM;
Reverse screening on indicaxanthin from Opuntia ficus-indica as natural chemoactive and chemopreventive agent
Keywords: Phytochemicals; Indicaxanthin; Neuromodulator; Anti-inflammatory agent; Anti-cancer; Reverse screening; Pharmacophore modeling; Docking; Molecular dynamics; MM-GBSA;
Comparative subtractive proteomics based ranking for antibiotic targets against the dirtiest superbug: Acinetobacter baumannii
Keywords: Acinetobacter baumannii; Subtractive proteomics; KdsA enzyme; AutoDock Vina; GOLD; Inhibitor-4636; MM-GBSA;
Computational and synthetic approaches for developing Lavendustin B derivatives as allosteric inhibitors of HIV-1 integrase
Keywords: HIV-1; Integrase; LEDGF/p75; ALLINI; Computational studies; IN-LEDGF/p75 binding; ALLINI; allosteric integrase inhibitor; CCD; catalytic core domain; CTD; C-terminal domain; IBD; IN-binding domain; IN; Integrase; INLAIs; Integrase lens epithelium-derived
Pterostilbene-mediated Nrf2 activation: Mechanistic insights on Keap1:Nrf2 interface
Keywords: PTS; pterostilbene; ARE; antioxidant responsive element; Keap1; Kelch-like ECH-associated protein-1; Nrf2; nuclear factor erythroid 2-related factor 2; MIN6 cells; mouse insulinoma-6 cells; MD; molecular dynamics; RMSD; root-mean square deviation; MM-GBSA
The solvent at antigen-binding site regulated C3d-CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation
Keywords: C3d; Complement; CR2; Molecular dynamics simulation; MM-GBSA;
Molecular dynamics simulation and free energy calculation studies of kinase inhibitors binding to active and inactive conformations of VEGFR-2
Keywords: VEGFR-2; Type I inhibitors; Type II inhibitors; Molecular dynamics; MM-PBSA; MM-GBSA
A theoretical view of the C3d:CR2 binding controversy
Keywords: C3d; complement fragment 3d; CR2; complement receptor 2; SCR; short consensus repeat; PDB; protein data bank; MD; molecular dynamics; SASA; solvent-accessible surface area; SMD; steered molecular dynamics; AESOP; analysis of electrostatic similarities of
Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation
Keywords: Bcl-xl; MD simulations; Free energy; MM-GBSA; Ligand; Interfacial waterΔG, binding free energy; ΔE, change in enthalpy; ΔΔETot, change in enthalpy in presence of selected explicit water–change in enthalpy in complete implicit environment; ABNR, adopted ba
Insight into the interaction mechanism of inhibitors P4 and WK23 with MDM2 based on molecular dynamics simulation and different free energy methods
Keywords: MD simulation; p53-MDM2 interaction; Binding free energy; MM-GBSA; SIE method;
Discovery of potential and selective COX-1 inhibitory leads using pharmacophore modelling, in silico screening and in vitro evaluation
Keywords: COX; 3D QSAR; MM-GBSA; Docking; PHASE; Decoy
In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction
Keywords: CDK9, cyclin-dependent kinase 9; aMD, accelerated molecular dynamics; MM-GBSA, molecular mechanics generalized Born surface areaCDK9/cyclin T1; Druggability mapping; Protein–protein interactions; Accelerated molecular dynamics; MM-GBSA
New scaffolds of natural origin as Integrase-LEDGF/p75 interaction inhibitors: Virtual screening and activity assays
Keywords: HIV-1 Integrase; LEDGF/p75; Protein-protein interaction inhibitors; LEDGINs; Natural products; Virtual screening; AIDS; acquired immunodeficiency syndrome; CCD; catalytic core domain; HIV-1; human immunodeficiency virus type 1; IBD; integrase binding do
Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors
Keywords: Cell-cycle; Glide XP docking; MM-GBSA; Binding free energy; Biological activity;
Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2–p53 interaction
Keywords: MD simulations; MM-GBSA; Binding free energy; MDM2–p53 interaction; Conformational mobility
Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: Screening for novel inhibitor scaffolds
Keywords: trans-Sialidase; Pharmacophore; Docking; Molecular dynamics; MM-GBSA
Advances and applications of binding affinity prediction methods in drug discovery
Keywords: Binding affinity; Drug discovery; Virtual screening; Scoring functions; Free energy perturbation (FEP); Linear interaction energy (LIE); MM-PBSA; MM-GBSA; BEAR
Synthesis, in silico, in vitro, and in vivo investigation of 5-[11C]methoxy-substituted sunitinib, a tyrosine kinase inhibitor of VEGFR-2
Keywords: Sunitinib®; VEGFR; Docking; Molecular dynamics; MM-GBSA; Carbon-11; Radiolabeling
Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations
Keywords: VEGFR2; Semaxanib; CoMFA; Docking; Molecular dynamics; MM-GBSA
Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations
Keywords: Virtual screening; Post-docking refinement; MM-PBSA; MM-GBSA; Enrichment factor; Drug design
Investigation of the diastereomerism of dihydrobenzoxathiin SERMs for ER alpha by molecular modeling
Keywords: Estrogen receptor; Diastereomerism; SERMs; Molecular modeling; MM-GBSA; Dihydrobenzoxathiin
Identification of optimum computational protocols for modeling the aryl hydrocarbon receptor (AHR) and its interaction with ligands
Keywords: Aryl hydrocarbon receptor (AHR); Docking; Scoring; Molecular dynamics; MM-GBSA; CYP1A1; TCDD
Design, synthesis, biological evaluation and computational investigation of novel inhibitors of dihydrofolate reductase of opportunistic pathogens
Keywords: pc, Pneumocystis carinii; tg, Toxoplasma gondii; DHFR, dihydrofolate reductase; HIV, human immunodeficiency virus; ma, Mycobacterium aviumDihydrofolate reductase; 2,4-Diaminopyrimidine; Docking; MM-GBSA
Calculation of binding free energies for non-zinc chelating pyrimidine dicarboxamide inhibitors with MMP-13
Keywords: MMPs; Molecular dynamics; Protein–ligand binding; Energy decomposition; MM-GBSA
Molecular modeling of human cytochrome P450 2W1 and its interactions with substrates
Keywords: CYP2W1; Homology modeling; Molecular docking; Molecular dynamics simulation; MM-GBSA
Effect of mutation K85R on GSK-3β: Molecular dynamics simulation
Keywords: GSK-3β; K85R mutation; Molecular dynamics simulation; MM-GBSA