[PDF] Top 20 Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
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Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
... found to be directly tethered to a divalent metal cation (assumed to be Zn 2+ ) ...the nicotinamidase from Streptococcus pneumoniae (SpNic) in unliganded and ligand-bound forms, even ... See full document
12
Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.
... detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD) simulations and free energy calculations were used to elucidate the mechanism about the effect of ... See full document
15
IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
... used to assess the solvation effect (Kollman et ...screening to improve the predictions of bound conformations (Charifson et ...the ligand-binding process is cooperatively driven by enthalpic ... See full document
18
Molecular determinants of epidermal growth factor binding: a molecular dynamics study.
... requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase ...known to bind EGFR ... See full document
12
Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding.
... conformational dynamics of the protein and interplay between ligand ...used molecular modeling and docking based approaches to unravel questions like differences in ligand ... See full document
17
Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs).
... found to be associated with CAG trinucleotide repeat ...the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(CAG) ...effects. To discern the role of ... See full document
15
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
... had to adjust the system size ...NVT dynamics (constant volume and temperature) is used for the first and second steps, and the NPAT (constant pressure, area, and temperature) dynamics for the rest ... See full document
9
J. Braz. Chem. Soc. vol.28 número7
... the molecular surface of BSA for the PIA pose with the best docking ...protein binding site, which could be related to the high binding constants values obtained in the fluorescence quenching ... See full document
8
Explicit and implicit modeling of nanobubbles in hydrophobic confinement
... seems to be important for the control of physio- logical ion ...have to de- solvate to travel through the ...sensitive to local geom- etry and electrostatics, implying that it can play a key ... See full document
10
Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.
... photo-switching simulations adopted a protocol used previously on this system, where a short biasing potential simulates the ligand photo-reaction and the following slow protein response can then be ... See full document
10
Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
... the binding residues was performed to evaluate the energetic effect of each residue on the binding ...MD simulations with standard deviation were shown in Figure ...for binding which is ... See full document
13
Lat. Am. j. solids struct. vol.14 número8
... 6-12) to explore some general trends of the small-scale impact fragmentation of a slender projectile at ultrahigh striking ...is to study inhomogeneous fragmentation with no assumptions made about ... See full document
18
Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets
... optimisation to establish a binding ...used to accept this or ...dedicated to the docking of small molecules on target ...the ligand input files (Grosdidier et ...contrast to ... See full document
10
Stability of intrinsically disordered regions of two transcription factors by molecular dynamics
... tendency to develop beta-structures, such as β-sheets and β- turns, has been described as another ...propensity to create structures of the amyloid kind ...tion to these illnesses, Intrinsically ... See full document
58
Mapping the structural and dynamical features of kinesin motor domains.
... used to evaluate the overall conformational space sampled by each set of simulations (Figure ...of simulations sampled a wide region of conformational space, but that nucleotide free systems covered ... See full document
13
Dynamic allostery in the methionine repressor revealed by force distribution analysis.
... calculations to calculate ESP charges on the SAM/SAH atoms and all QM calculations were carried out using Gaussian03 ...used to perform single energy ...fitting to the electrostatic potential at ... See full document
11
Ana Sofia Fernandes de Oliveira
... ATP binding is essential for the formation of the closed NBD dimer, with the two ATP molecules functioning as a molecular “glue”, keeping the catalytic monomers close together [35, 56, ...started to ... See full document
269
Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.
... protein kinase (PK) that regulates glycogen, sugar, and lipid metabolism. The selectivity of PKA is essential for cell integrity. It phosphorylates specific targets in the cell that contain a sequence pattern in the ... See full document
14
J. Braz. Chem. Soc. vol.24 número4
... results show that the energies increase along with the number of coordinated nitrate anions replacing the DBM ligand in the complexes. The luminescence spectra and emission lifetime measurements revealed that the ... See full document
8
Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.
... nodes to connect the FTP severer using the bundle of verified message and to download the ligands into the local machine ...automatically. To make sure the transferring security of the message, ... See full document
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