Keywords: FPL; Acetylcholinesterase; AMBER; CHARMM; OPLS; GROMOS;
مقالات ISI (ترجمه نشده)
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Keywords: Force field; Docking; Quantum chemistry; MMFF94; CHARMM; PM7; PM6; Supercomputer;
Keywords: Force-field optimization; Molecular dynamics; Neutron data analysis; Quasi-elastic neutron scattering; Biopolymers; CHARMM;
Keywords: Ã
; Angstrom; AFM; atomic force microscopy; AMBER; Assisted Model Building and Energy Refinement R. Salomon-Ferrer, D.A. Case, R.C. Walker, An overview of the Amber biomolecular simulation package, WIREs Comput. Mol. Sci. 3 (2012) 198-210; BSA; Bovine s
The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases
Keywords: B3LYP; Becke 3 parameter Lee - Yang - Parr functional; CA; carbonic anhydrase; CHARMM; Chemistry at HARvard Molecular Mechanics; DFT; density functional theory; FF; force field; MD; Molecular Dynamics; NAMD; Nanoscale Molecular Dynamics; NBO; Natural
Selective ion binding and transport by membrane proteins - A computational perspective
Keywords: ABF; Adaptive Biasing Force; ADP; Adenosine Diphosphate; aHL; alpha-Hemolysin; AMBER; Assisted Model Building with Energy Refinement; AMP; Adenosine Monophosphate; AMOEBA; Atomic Multipole Optimized Energetics for Biomolecular Simulation; ATP; Adenosine T
Keywords: Graphene oxide; Molecular dynamics; REBO-CHO; COMB3; CHARMM;
Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field
Keywords: CHARMM; MD simulations; Carbohydrates; Monosaccharides; Molecular mechanics;
Ligand-dependent modulation of hOCT1 transport reveals discrete ligand binding sites within the substrate translocation channel
Keywords: OCT1; Organic Cation Transporter 1; hOCT1; human OCT1; HEK; Human Embryonic Kidney; EV; empty vector; MPP+; 1-methyl-4-phenylpyridinium; TEA; tetraethylammonium; CCF; competitive counter flow; TMD; transmembrane domains; CHARMm; Chemistry at Harvard Macro
Performance of various models in structural characterization of n-butanol: Molecular dynamics and X-ray scattering studies
Keywords: GROMOS; CHARMM; OPLS; AMBER; TraPPE; Complemented system approach;
Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity
Keywords: CHARMM; chemistry at Harvard molecular mechanics; DNA; deoxyribonucleic acid; MD; molecular dynamics; NMR; nuclear magnetic resonance; MMTSB; multi-scale modeling tools in structural biology; MSM; Markov state model; NAMD; nanoscale molecular dynamics; NP
In silico identification of novel antagonists and binding insights by structural and functional analyses of guanylate kinase of Leishmania donovani and interaction with inhibitors
Keywords: GK; guanylate kinase; VL; visceral leishmaniasis; GMPK; guanosine monophosphate kinase; 5GP; 5â²-guanylic acid; GOLD; genetic optimization for ligand docking; CHARMM; chemistry of HARvard molecular mechanics; BLAST; basic local alignment search tool; PDB
Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22
Keywords: CHARMM; Force field parameterization; Quantum mechanics; Molecular dynamics; Potential energy surface; Geometry optimization;
Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions
Keywords: Sigma hole; Halogen bond; CHARMM; Halogen; Drug design; CGenFF;
Imidacloprid and thiacloprid neonicotinoids bind more favourably to cockroach than to honeybee α6 nicotinic acetylcholine receptor: Insights from computational studies
Keywords: nAChR; nicotinic acetylcholine receptor; Ac-AChBP; Aplysia californica-acetylcholine binding protein; LGICs; ligand-gated ion channels; GABA; gamma-aminobutyric acid; 5-HT3; 5-hydroxytryptamine receptor subtype 3; CHARMM; Chemistry at Harvard Molecular Me
Mechanisms of DNA methyltransferase-inhibitor interactions: Procyanidin B2 shows new promise for therapeutic intervention of cancer
Keywords: DNMT; DNA methyltransferases; EGCG; epigallocathechin-3-gallate; SAH; S-Adnosyl-l-homocysteine; ChEBI; chemical entities of biological interest; PDB; protein data bank; UniProt; the Universal Protein knowledgebase; CHARMm; chemistry at HARvard molecular m
The binding mechanisms of plasma protein to active compounds in Alismaorientale rhizomes (Alismatis Rhizoma)
Keywords: SDS-PAGE; sodium dodecyl sulfate-polyacrylamide gel electrophoresis; CD; circular dichroism; CHARMm; Chemistry at HARvard Macromolecular Mechanics; Hb; hemoglobin; PBS; phosphate buffered saline; PDB; Protein Data Bank; RMSD; relative mean standard de
Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification
Keywords: AT; aminotetralines; BFZ; bifonazole; BH; benzoheterocycles; BP; benzopyrones; CHARMM; Chemistry at HARvard Macromolecular Mechanics; CoMFA; comparative molecular field analysis; CPR; NADPH-cytochrome P450 oxidoreductase; CR; chromanes; CTZ; clotrimazole;
Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation
Keywords: CHARMM; Chemistry at Harvard Macromolecular Mechanics; EPR; electron paramagnetic resonance; FTIR; Fourier transform infrared; GPCR; G protein-coupled receptor; MD; molecular dynamics; Meta I; metarhodopsin I; Meta II; metarhodopsin II; 2MBD; 2-methyl-but
Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions
Keywords: MALDI; Molecular dynamics (MD) simulations; CHARMM; Amino acid (AA); 2,5-Dihydroxybenzoic acid (DHB); Binding energy (BE);
Structural analysis of a group III Glu62-phospholipase A2 from the scorpion, Mesobuthus tamulus: Targeting and reversible inhibition by native peptides
Keywords: PLA2; phospholipase A2; ExPASy; Expert Protein Analysis System; DS; Discovery Studio; ABNR; adopted basis set Newton-Raphson; CHARMM; Chemistry at HARvard Molecular Mechanics; PROCHECK; protein structure check; r.m.s.d.; root mean square deviation; ps;
A molecular dynamics model of the Bt toxin Cyt1A and its validation by resonance energy transfer
Keywords: Bacillus thuringiensis toxin; CHARMM; NAMD; Mutation; Computer simulation; Resonance energy transfer;
A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis
Keywords: Ricin-A-chain; Depurination mechanism; CHARMM; Normal modes analysis; Terahertz spectroscopy
State conditions transferability of vapor–liquid equilibria via fluctuation solution theory with correlation function integrals from molecular dynamics simulation
Keywords: Fluctuation solution theory; CHARMM; Molecular dynamics
QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface
Keywords: Hybrid QM/MM simulation; IMOMM; CHARMM; Histidine; Chelate; Adhesion