Keywords: دینامیک مولکولی یا پویایی مولکولی; 7HC, 7-hydroxycoumarin; Cbz, carbobenzyloxy; TG2, tissue transglutaminase; MD, molecular dynamics; GABA, γ-aminobutyric acid; gTG2, guinea pig liver transglutaminase; NTA, nitrilotriacetic acid; MOPS, 3-(N-morpholino) propanesulfonic acid; EDTA, ethylened
مقالات ISI دینامیک مولکولی یا پویایی مولکولی (ترجمه نشده)
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Keywords: دینامیک مولکولی یا پویایی مولکولی; MD, molecular dynamics; SASA, Solvent Accessible Surface Area; RMSD, Root Mean Square Deviation; STI, Soybean Trypsin Inhibitor; KTI, Kunitz-type Trypsin Inhibitor; NMR, Nuclear Magnetic Resonance Imaging; VMD, Visual Molecular Dynamics; FTIR, Fourier Tra
Keywords: دینامیک مولکولی یا پویایی مولکولی; TF, trigger factor; RBD, ribosome-binding domain; PPIase, peptidyl-prolyl cis/trans-isomerase; MST, microscale thermophoresis; MD, molecular dynamics; NC, nascent chain; cryo-EM, cryo-electron microscopy; GatD, galactitol-1-phosphate dehydrogenase; RNCs,
Keywords: دینامیک مولکولی یا پویایی مولکولی; EV, enterovirus; CI, capsid-binding inhibitors; VP1–4, viral capsid protein 1–4; CVB3, coxsackievirus B3; HPLC, high performance liquid chromatography; MD, molecular dynamics; moi, multiplicity of infection; PME, particle mesh Ewald; RMSD, root-mean-squar
Keywords: دینامیک مولکولی یا پویایی مولکولی; cuCES, chicken uropygial carboxylesterase; hCES1, human carboxylesterase 1; MD, molecular dynamics; RMSF, root-mean-square fluctuationChicken uropygial carboxylesterase; Nucleotide sequencing; 3D structure modeling; Thermostability; Molecular dynamic; Doc
Keywords: دینامیک مولکولی یا پویایی مولکولی; MD, molecular dynamics; CPD, computational protein design; YFP, yellow fluorescent protein; FRET, Förster resonance energy transfer; rmsf, root-mean-square fluctuationmolecular dynamics; computational protein design; in silico screening; homodimer; domain
Keywords: دینامیک مولکولی یا پویایی مولکولی; ENM, elastic network model; RENM, robust elastic network model; VDOS, vibrational density of states; ADPs, anisotropic displacement parameters; MD, molecular dynamics; CG, coarse-grained; NM, normal mode; ANM, anisotropic network model; GNM, Gaussian netw
Keywords: دینامیک مولکولی یا پویایی مولکولی; AU-ROC, area under receiver operator characteristic; DFT, density functional theory; MD, molecular dynamics; NSLR, normalized sum of the logarithm of ranks; NSMLR, normalized sum of the modified logarithm of ranks; PhK, phosphorylase kinase; QM/MM, quantu
Keywords: دینامیک مولکولی یا پویایی مولکولی; GAPD, glyceraldehyde-3-phosphate dehydrogenase somatic; GAPDS, sperm-specific glyceraldehyde-3-phosphate dehydrogenase; MD, molecular dynamics; DSC, differential scanning calorimetryGlyceraldehyde-3-phosphate dehydrogenase; Structural factors of stability
Keywords: دینامیک مولکولی یا پویایی مولکولی; TM, transmembrane; TMH, transmembrane helix; AP, arrest peptide; bR, bacteriorhodopsin; MP, membrane protein; ER, endoplasmic reticulum; MD, molecular dynamics; AFM, atomic force microscopy; PTC, polypeptide transferase center; SRP, signal recognition par
Keywords: دینامیک مولکولی یا پویایی مولکولی; rNTP, ribonucleotide; CPD<TT>, cis-syn cyclobutane pyrimidine dimer; 6-4<TT>, 6,4 pyrimidine-pyrimidone; dNTP, deoxyribonucleotide; RER, ribonucleotide excision repair; MD, molecular dynamics; NER, nucleotide excision repair; GG-NER, global genomic repair
Keywords: دینامیک مولکولی یا پویایی مولکولی; 3D, three-dimensional; FRET, fluorescence resonance energy transfer; IHC, inner hair cell; MD, molecular dynamics; NLC, nonlinear capacitance; OHC, outer hair cell; SulTP, sulfate transporter; STAS, sulfate transporter and antisigma-factor antagonist; TM,
Keywords: دینامیک مولکولی یا پویایی مولکولی; OAYGJRKNPJYYDM-STZJPYNISA-N; OAYGJRKNPJYYDM-MLRPVWBGSA-N; WPOJGFFRLTUTKV-ANWLOKAESA-N; RNCAUFATXCGLID-ZWMWCNLPSA-N; RNCAUFATXCGLID-JJARWVHBSA-NGlcNAc, N-acetylglucosamine; MD, molecular dynamics; MurNAc, N-acetylmuramic acid; RMSd, root mean square deviat
Keywords: دینامیک مولکولی یا پویایی مولکولی; δ-ALA, δ-aminolevulinic acid; BSTFA, N,O-bis(trimethylsilyl)trifluoroacetamide; CPR, NADPH-P450 reductase; CYP102A1, Cytochrome P450 BM3; IPTG, isopropyl-β-d-thiogalactopyranoside; MD, molecular dynamics; P450 or CYP, cytochrome P450; PCR, polymerase chai
Structural determinants of subtype selectivity and functional activity of angiotensin II receptors
Keywords: دینامیک مولکولی یا پویایی مولکولی; AngII, angiotensin II; AT1, angiotensin II receptor type 1; AT2, angiotensin II receptor type 2; GPCR, G-protein coupled receptor; TM, transmembrane domain; EL, extracellular loop; IL, intracellular loop; MD, molecular dynamics; NMR, nuclear magnetic reso
Difference in DNA-binding abilities of Fur-homolog DNA binding protein from Neisseria gonorrhoeae
Keywords: دینامیک مولکولی یا پویایی مولکولی; Gonorrhea; TF; Computational modelling; Molecular docking simulations; Molecular dynamicsTF, Transcription Factor; PDB, Protein Data Bank; BLAST, Basic Local Alignment Search Tool; RMSD, Root Mean Squared Deviation; MD, Molecular Dynamics
Malony-CoA inhibits the S113L variant of carnitine-palmitoyltransferase II
Keywords: دینامیک مولکولی یا پویایی مولکولی; CoA, coenzyme A; CPT I, carnitine palmitoyltransferase I; CPT II, carnitine palmitoyltransferase II; hCPT2, gene coding for human muscle carnitine palmitoyltransferase II; MD, molecular dynamics
In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1
Keywords: دینامیک مولکولی یا پویایی مولکولی; ADAM, a disintegrin and metalloproteinase; ADAMTS, ADAM with thrombospondin domains motifs; ECM, extracellular matrix; LAP, latency-associated protein; LGAL, amarckian genetic algorithm; Kd, dissociation constant; MD, molecular dynamics; RMSD, root mean s
Highly selective separation and adsorption-induced phase transition of SF6-N2 fluid mixtures in three-dimensional carbon nanotube networks
Keywords: دینامیک مولکولی یا پویایی مولکولی; PNN, porous nanotube network; MD, molecular dynamics; GCMC, grand canonical monte carlo; rdf, radial distribution function; tcf, time correlation functionSeparation process; Adsorption; Sulfur hexafluoride; Nitrogen; Porous nanotube networks; Molecular dy
Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface
Keywords: دینامیک مولکولی یا پویایی مولکولی; CL, cytoplasmic loop; Cx, connexin; DOPE, discrete optimized protein energy; E2, second extracellular loop; HB, hydrogen bond; hCx, human connexin; MD, molecular dynamics; SCAM, substituted cysteine accessibility method; wt, wild type
Physical characterization and in silico modeling of inulin polymer conformation during vaccine adjuvant particle formation
Keywords: دینامیک مولکولی یا پویایی مولکولی; SAXS, small angle X-ray scattering; FTIR ATR, attenuated total reflectance Fourier transform infrared; AFM, atomic force microscopy; TEM, transmission electron microscopy; PBS, phosphate buffered saline; MD, molecular dynamics; DFT, density functional the
Crystal structure and dynamics of Spt16N-domain of FACT complex from Cicer arietinum
Keywords: دینامیک مولکولی یا پویایی مولکولی; PDB, protein data bank; MD, molecular dynamics; NMA, normal mode analysis; ENM, elastic network model; Spt16Nca, N-terminal domain of Spt16 from Cicer arietinum; Spt16Nsp, N-terminal domain of Spt16 from Schizosaccharomyces pombe; Spt16Nsc, N-terminal dom
Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII
Keywords: دینامیک مولکولی یا پویایی مولکولی; LSD, lysosomal storage disease; MPSVII, mucopolysaccharidosis type VII; MD, molecular dynamics; GUSB, β-glucuronidase; WT, wild type; RMSD, root mean square deviations; RMSF, root mean square fluctuations; Rg, radius of gyration; ns, nano secondLysosomal
Binding mode prediction of aplysiatoxin, a potent agonist of protein kinase C, through molecular simulation and structure–activity study on simplified analogs of the receptor-recognition domain
Keywords: دینامیک مولکولی یا پویایی مولکولی; ATX, aplysiatoxin; PKC, protein kinase C; DAT, debromoaplysiatoxin; DAG, 1,2-diacyl-sn-glycerol; RD, recognition domain; MM, molecular mechanics; DFT, density functional theory; MD, molecular dynamics; POPS, 1-palmitoyl-2-oleoyl-phosphatidylserine; Kd, di
Advances in the surface defect machining (SDM) of hard steels
Keywords: دینامیک مولکولی یا پویایی مولکولی; AISI, American Iron and Steel Institute; CBN, cubic boron nitride; CNC, computer numerically controlled; FEA, finite element analysis; HT, hard turning; HRC, Rockwell C scale hardness; MD, molecular dynamics; SDM, surface defect machiningSurface defect ma
Design of cholesterol arabinogalactan anchored liposomes for asialoglycoprotein receptor mediated targeting to hepatocellular carcinoma: In silico modeling, in vitro and in vivo evaluation
Keywords: دینامیک مولکولی یا پویایی مولکولی; ASGPR, asialoglycoprotein receptor; LDS, liposomal delivery systems; HCC, hepatocellular carcinoma; MD, molecular dynamics; AG, arabinogalactan; Chol, cholesterol; CHOL-AL-AG, cholesteryl arabinogalactan; DSPC, distearoylphosphatidylcholine; EE, entrapmen
Investigating molecular dynamics-guided lead optimization of EGFR inhibitors
Keywords: دینامیک مولکولی یا پویایی مولکولی; EGFR, epidermal growth factor receptor; MD, molecular dynamics; MM/GBSA, molecular mechanics/generalized born surface area; MM/PBSA, molecular mechanics/Poisson–Boltzmann surface area; TK, tyrosine kinase; GAFF, generalized amber force field; SASA, solven
Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor – An Insight through molecular dynamics and docking approach
Keywords: دینامیک مولکولی یا پویایی مولکولی; ID, Inhibitors of DNA binding protein; ID3, Inhibitor of DNA binding protein 3; E2A, Transcription factor E2-alpha; BHLH, Basic Helix–Loop–Helix; MD, Molecular dynamics; PCA, Principal Component Analysis; FEL, Free Energy LandscapeInhibitor of DNA binding
Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis
Keywords: دینامیک مولکولی یا پویایی مولکولی; MD, molecular dynamics; DM, double mutant; RMSD, root mean square deviation; RMSF, root mean square fluctuationDocking; Simulation; Pyrazinamide; RMSD; RMSF
Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations
Keywords: دینامیک مولکولی یا پویایی مولکولی; SDH, sorbitol dehydrogenase; MDH, mannitol dehydrogenase; MD, molecular dynamics; QPLD, quantum polarized ligand docking; XP, extra precision; SP, standard precision; QM, quantum mechanics; MM, molecular mechanicsSorbitol dehydrogenase; d-sorbitol; l-sorb
Structural and biochemical characterization of two heme binding sites on α1-microglobulin using site directed mutagenesis and molecular simulation
Keywords: دینامیک مولکولی یا پویایی مولکولی; A1M, α1-microglobulin; AMBP, A1M-bikunin precursor protein; IgA, immunoglobulin A; ROS, reactive oxygen species; FPLC, fast protein liquid chromatography; SPR, surface plasmon resonance; MD, molecular dynamics; CD, circular dichroism; RMSD, root mean squa
Study of early stages of amyloid Aβ13-23 formation using molecular dynamics simulation in implicit environments
Keywords: دینامیک مولکولی یا پویایی مولکولی; Aβ, β-amyloid; AD, Alzheimer’s disease; APP, amyloid precursor protein; DOPS, dioleoylphosphatidylserine; DPPC, dipalmitoylphosphatidylcholine; HBimbb, intermolecular backbone hydrogen bonds; HFIP, hexafluoroisopropanol; MD, molecular dynamics; PDB, Prote
Integration of inhibition kinetics and molecular dynamics simulations to determine the effects of Zn2+ on acetaldehyde dehydrogenase 1
Keywords: دینامیک مولکولی یا پویایی مولکولی; Acetaldehyde dehydrogenase 1; Zn2+; Inhibition kinetics; Molecular dynamicsALDH1, acetaldehyde dehydrogenase 1; ANS, 1-anilinonaphthalene-8-sulfonate; MD, molecular dynamics
Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase
Keywords: دینامیک مولکولی یا پویایی مولکولی; MD, molecular dynamics; PE, phosphatidylethanolamine; PC, phosphatidylcholine; CL, cardiolipin; CcO, cytochrome c oxidaseMolecular dynamics simulation; Continuum electrostatic; Water molecule; Oxygen diffusion; Cardiolipin
Hardening due to dislocation loop damage in RPV model alloys: Role of Mn segregation
Keywords: دینامیک مولکولی یا پویایی مولکولی; RPV, reactor pressure vessel; LWR, light water reactor; TEM, transmission electron microscopy; CRP, copper rich precipitates; MNP, Manganese–Nickel precipitates; PAS, positron annihilation spectroscopy; MD, molecular dynamics; DL, dislocation loop; PWR, p
Effect of thermal and electric field treatment on the conformation of Ara h 6 peanut protein allergen
Keywords: دینامیک مولکولی یا پویایی مولکولی; IgE, Immunoglobulin E; SASA, Solvent Accessible Surface Area; RMSD, Root Mean Square Deviation; SR, Systemic Allergic Reaction; OAS, Oral Allergy Syndrome; NMR, Nuclear Magnetic Resonance Imaging; MD, Molecular Dynamics; FTIR, Fourier Transformation Infra
Perspective on computational and structural aspects of kinase discovery from IPK2014
Keywords: دینامیک مولکولی یا پویایی مولکولی; Abl, Abelson murine leukemia; MD, Molecular dynamics; Melk, Maternal embryonic leucine zipper kinase; Kit, v-kit Hardy–Zuckerman 4 feline sarcoma viral oncogene homolog; JNK, c-Jun N-terminal kinase; PLK, Polo like kinase; CDK, Cyclin dependent kinase; ER
Molecular docking and molecular dynamics simulation studies of Trypanosoma cruzi triosephosphate isomerase inhibitors. Insights into the inhibition mechanism and selectivity
Keywords: دینامیک مولکولی یا پویایی مولکولی; TcTIM, Trypanosoma cruzi triosephosphate isomerase; hTIM, Homo sapiens triosephosphate isomerase; MD, molecular dynamics; SD, steepest descent; CG, conjugate gradient; SASA, solvent accessible surface areaMolecular docking; Molecular dynamics; Selective T
Populus deltoides Kunitz trypsin inhibitor 3 confers metal tolerance and binds copper, revealing a new defensive role against heavy metal stress
Keywords: دینامیک مولکولی یا پویایی مولکولی; GFP, green fluorescent protein; KTI, Kunitz trypsin inhibitor; MD, molecular dynamics; PDB, Protein Data Bank; Populus deltoides KTI3, (PdKTI3); PI, proteinase inhibitor; RT-PCR, reverse transcription PCR; SD, synthetic defined; YPD, yeast potato dextrose
Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken
Keywords: دینامیک مولکولی یا پویایی مولکولی; FCR, feed conversion ratio; MD, molecular dynamics; SIFT, sorting intolerant from tolerant; SNP, single nucleotide polymorphism; nsSNPs, non-synonymous single nucleotide polymorphisms; AASs, amino acid substitutions; TGFB, transforming growth factor beta;
Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii
Keywords: دینامیک مولکولی یا پویایی مولکولی; OM, outer membrane; MD, molecular dynamics; SeMet, selenomethionine; CV, column volumes; PEG, polyethylene glycolAcinetobacter baumannii; outer membrane protein; crystal structure; small molecule uptake; antibiotic resistance
Structure of Hepatitis C Virus Envelope Glycoprotein E1 Antigenic Site 314–324 in Complex with Antibody IGH526
Keywords: دینامیک مولکولی یا پویایی مولکولی; HCV, hepatitis C virus; mAb, monoclonal antibody; MD, molecular dynamics; DMF, N,N-dimethylformamide; TFA, trifluoroacetic acid; APS, Advanced Photon Source; vdW, van der WaalsHCV; E1 envelope glycoprotein; IGH526; vaccine design
Elastic deformation and area per lipid of membranes: Atomistic view from solid-state deuterium NMR spectroscopy
Keywords: دینامیک مولکولی یا پویایی مولکولی; DMPC-d54, 1,2-diperdeuteriomyristoyl-sn-glycero-3-phosphocholine; DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine; GPCR, G-protein-coupled receptor; MD, molecular dynamics; NMR, nuclear magnetic resonance; PEG, polyethylene glycol; RQC, residual quadrup
Stabilization of cyclohexanone monooxygenase by a computationally designed disulfide bond spanning only one residue
Keywords: دینامیک مولکولی یا پویایی مولکولی; BVMO, Baeyer–Villiger monooxygenase; CHMO, cyclohexanone monooxygenase; DTT, dithiothreitol; MD, molecular dynamics; PAMO, phenylacetone monooxygenaseBaeyer–Villiger monooxygenase; Computational design; Disulfide bonds; Thermostability; Flavoprotein; Enzy
Origin of ion selectivity in Phaseolus coccineus mitochondrial VDAC
Keywords: دینامیک مولکولی یا پویایی مولکولی; BD, Brownian Dynamics; GHK, Goldman–Hodgkin–Katz; LCT, large channel theory; mVDAC1, mouse VDAC isoform 1; MD, molecular dynamics; NcVDAC, Neurospora crassa VDAC; OMM, outer mitochondrial membrane; ScVDAC1, Saccharomyces cerevisiae VDAC isoform 1; TMS, Te
Syntheses of coumarin–tacrine hybrids as dual-site acetylcholinesterase inhibitors and their activity against butylcholinesterase, Aβ aggregation, and β-secretase
Keywords: دینامیک مولکولی یا پویایی مولکولی; AD, Alzheimer’s disease; AChE, acetylcholinesterase; BChE, butylcholinesterase; ACh, acetylcholine; Aβ, amyloid-β; CAS, catalytic active site; PAS, peripheral active site; MD, molecular dynamics; ATC, acetylthiocholine; ESI-MS, electrospray ionisation mas
Interaction of anticancer reduced Schiff base coumarin derivatives with human serum albumin investigated by fluorescence quenching and molecular modeling
Keywords: دینامیک مولکولی یا پویایی مولکولی; CS, conformational search; D, distribution coefficient; HSA, human serum albumin; ICT, intramolecular charge transfer; λEM, fluorescence emission wavelength; λEX, fluorescence excitation wavelength; MD, molecular dynamics; MM–PBSA, molecular mechanics–Poi
Creation of thermostable and alkaline stable xylanase variants by DNA shuffling
Keywords: دینامیک مولکولی یا پویایی مولکولی; StEP, staggered extension process; MD, molecular dynamics; IPTG, isopropylthiogalactosideDNA shuffling; Staggered extension process; Xylanase; T. lanuginosus; Stability
Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations
Keywords: دینامیک مولکولی یا پویایی مولکولی; MD, molecular dynamics; RMSF, root mean square fluctuation; RMSD, root mean square deviation; RMSIP, root mean square inner product; ITC, isothermal titration calorimetry; PDB, Protein Data Bank; INC, insomniac protein; Cul3, Cullin3; CRL, Cullin RING lig
Flipping of the Ribosomal A-Site Adenines Provides a Basis for tRNA Selection
Keywords: دینامیک مولکولی یا پویایی مولکولی; CPD, center-of-mass pseudo-dihedral angle; 2D, two-dimensional; MD, molecular dynamics; RMSF, root-of-mean-square fluctuation; TI, thermodynamic integrationribosome; A-site; decoding; tRNA selection